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/7787361/working' mkdir: created directory `/scratch/stefan/7787361/working/protonate' Storing results in /scratch/stefan/7787361/finished Working in /scratch/stefan/7787361/working /scratch/stefan/7787361/working /scratch/stefan/7787361 /scratch/stefan/7787361/working/protonate /scratch/stefan/7787361/working /scratch/stefan/7787361 Precomputing protomers for all compounds (pH: 7.4) ph 7.4: 1035 protomers created Coalesing and merging protomers 1016 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1028 protomers after new stereo-center expansion /scratch/stefan/7787361/working /scratch/stefan/7787361 Bulk generating 3D conformations all protomers in /scratch/stefan/7787361/working/3D mkdir: created directory `/scratch/stefan/7787361/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7787361/working/protonate/xaaaabe-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' 1029 3D conformations generated for 1000 compounds Building REAL300025580507 mkdir: created directory `/scratch/stefan/7787361/working/building' mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580507' /scratch/stefan/7787361/working/building/REAL300025580507 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580507 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580507/0 /scratch/stefan/7787361/working/building/REAL300025580507 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1 `/scratch/stefan/7787361/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC(=O)NCCC1=NC(=O)O[N-]1)NC(=O)OC(C)(C)C) `REAL300025580507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580507 none CC(CCC(=O)NCCC1=NC(=O)O[N-]1)NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 96, 74, 28, 28, 28, 13, 7, 1, 1, 1, 1, 1, 1, 1, 133, 169, 201, 201, 201, 201, 201, 201, 133, 133, 133, 133, 96, 96, 74, 74, 28, 13, 13, 7, 7, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 902 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580507 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580507 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `/scratch/stefan/7787361/finished' Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580507/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580507 Building REAL300025580508 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580508' /scratch/stefan/7787361/working/building/REAL300025580508 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580508 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580508/0 /scratch/stefan/7787361/working/building/REAL300025580508 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/2 `/scratch/stefan/7787361/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC(OC)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580508 none CCCOC1=CC(OC)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 154, 100, 100, 100, 59, 100, 144, 100, 100, 45, 46, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 186, 186, 100, 144, 144, 144, 100, 100, 45, 9, 9, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 809 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580508 none CCCOC1=CC(OC)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 6, 6, 6, 23, 23, 100, 100, 100, 100, 100, 38, 38, 38, 38, 38, 23, 23, 1, 3, 3, 3, 1, 1, 6, 23, 23, 23, 23] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 9, 10, 11, 12, 35, 30] set([0, 1, 2, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580508 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580508 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580508/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580508 Building REAL300025580509 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580509' /scratch/stefan/7787361/working/building/REAL300025580509 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580509 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580509/0 /scratch/stefan/7787361/working/building/REAL300025580509 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/3 `/scratch/stefan/7787361/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(OC(C)C)=C1) `REAL300025580509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580509 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(OC(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 154, 93, 154, 154, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 154, 154, 192, 201, 201, 154, 180, 180, 180, 154, 154, 49, 8, 8, 8, 8, 201, 201, 201, 201, 201, 201, 201, 154] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 656 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580509 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(OC(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 47, 47, 154, 154, 154, 154, 154, 1, 1, 7, 15, 15, 1, 3, 3, 3, 1, 1, 12, 47, 47, 47, 47, 15, 15, 15, 15, 15, 15, 15, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 17, 18, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 356 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580509 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580509 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580509/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580509 Building REAL300025580510 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580510' /scratch/stefan/7787361/working/building/REAL300025580510 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580510 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580510/0 /scratch/stefan/7787361/working/building/REAL300025580510 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/4 `/scratch/stefan/7787361/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1F) `REAL300025580510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580510 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 22, 22, 22, 79, 94, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 79, 79, 94, 94, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 547 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580510 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 52, 177, 52, 52, 17, 8, 1, 1, 1, 1, 1, 1, 1, 177, 201, 201, 195, 201, 201, 201, 201, 177, 177, 177, 177, 177, 177, 52, 17, 17, 8, 8, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580510 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580510 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580510/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580510 Building REAL300025580511 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580511' /scratch/stefan/7787361/working/building/REAL300025580511 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580511 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580511/0 /scratch/stefan/7787361/working/building/REAL300025580511 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/5 `/scratch/stefan/7787361/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=C2C(F)(F)F)O1) `REAL300025580511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580511 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=C2C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 5, 19, 19, 76, 103, 201, 201, 201, 201, 201, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 19, 76, 76, 103, 103, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 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]) total number of confs: 590 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580511 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=C2C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 35, 49, 139, 139, 139, 139, 139, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 5, 5, 5, 5, 1, 7, 34, 34, 49, 49, 1, 1, 5, 5, 2, 5] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 25, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580511 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=C2C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 74, 139, 139, 139, 139, 201, 201, 139, 201, 201, 201, 201, 201, 201, 139, 74, 23, 23, 8, 8, 139, 139, 201, 201, 186, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 699 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580511 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580511 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580511/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580511 Building REAL300025580512 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580512' /scratch/stefan/7787361/working/building/REAL300025580512 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580512 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580512/0 /scratch/stefan/7787361/working/building/REAL300025580512 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/6 `/scratch/stefan/7787361/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1=CC=CC=C1) `REAL300025580512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580512 none CC(C)N1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 4, 12, 4, 4, 4, 4, 4, 31, 31, 31, 106, 106, 158, 158, 158, 158, 158, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 4, 31, 106, 106, 106, 106, 1, 1, 1, 1, 1] 158 rigid atoms, others: [38, 39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 486 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580512 none CC(C)N1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [158, 149, 158, 149, 149, 149, 51, 51, 51, 8, 8, 1, 1, 1, 1, 1, 1, 1, 149, 149, 158, 158, 157, 158, 158, 158, 158, 158, 158, 158, 158, 158, 149, 50, 8, 8, 8, 8, 158, 158, 157, 158, 158] 158 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, 37, 38, 39, 40, 41, 42]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580512 none CC(C)N1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 1, 1, 1, 1, 1, 12, 12, 12, 65, 65, 149, 149, 149, 149, 149, 1, 1, 4, 4, 2, 4, 4, 6, 6, 5, 5, 6, 5, 6, 1, 12, 64, 64, 65, 65, 4, 4, 2, 4, 4] 158 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 18, 19] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580512 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580512 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580512/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580512 Building REAL300025580513 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580513' /scratch/stefan/7787361/working/building/REAL300025580513 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580513 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580513/0 /scratch/stefan/7787361/working/building/REAL300025580513 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/7 `/scratch/stefan/7787361/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(OCCOC(C)C)=C1) `REAL300025580513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580513 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(OCCOC(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 5, 5, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 81, 62, 81, 81, 36, 36, 36, 12, 7, 1, 1, 1, 1, 1, 1, 1, 81, 81, 97, 116, 120, 194, 201, 201, 81, 91, 91, 91, 81, 81, 36, 12, 12, 7, 7, 116, 116, 120, 120, 201, 201, 201, 201, 201, 201, 201, 81] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 641 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580513 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(OCCOC(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 5, 5, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 35, 81, 81, 81, 81, 81, 1, 1, 5, 13, 15, 40, 55, 55, 1, 3, 3, 3, 1, 1, 7, 33, 33, 35, 35, 13, 13, 15, 15, 55, 55, 55, 55, 55, 55, 55, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 47, 17, 18, 25, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580513 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580513 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580513/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580513 Building REAL300025580514 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580514' /scratch/stefan/7787361/working/building/REAL300025580514 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580514 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580514/0 /scratch/stefan/7787361/working/building/REAL300025580514 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/8 `/scratch/stefan/7787361/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1F) `REAL300025580514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580514 none CC(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 102, 102, 102, 102, 43, 43, 43, 23, 8, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 201, 201, 201, 201, 102, 102, 42, 23, 23, 8, 8, 102] 201 rigid atoms, others: [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: 584 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580514 none CC(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 53, 102, 102, 102, 102, 102, 1, 1, 1, 4, 4, 4, 4, 1, 1, 5, 29, 29, 53, 53, 1] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 19, 20, 21, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580514 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580514 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580514/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580514 Building REAL300025580515 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580515' /scratch/stefan/7787361/working/building/REAL300025580515 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580515 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580515/0 /scratch/stefan/7787361/working/building/REAL300025580515 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/9 `/scratch/stefan/7787361/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC([N+](=O)[O-])=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580515 none COC1=CC([N+](=O)[O-])=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 195, 195, 159, 195, 195, 195, 195, 195, 67, 67, 67, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 195, 195, 66, 20, 20, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 558 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580515 none COC1=CC([N+](=O)[O-])=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 12, 12, 12, 66, 78, 195, 195, 195, 195, 195, 3, 3, 3, 1, 1, 1, 12, 66, 66, 78, 78] 201 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 25, 26, 27] set([0, 32, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 471 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580515 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580515 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580515/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580515 Building REAL300025580516 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580516' /scratch/stefan/7787361/working/building/REAL300025580516 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580516 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580516/0 /scratch/stefan/7787361/working/building/REAL300025580516 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/10 `/scratch/stefan/7787361/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NCCC1=NC(=O)O[N-]1)C(=O)OCC1=CC=CC=C1) `REAL300025580516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580516 none CN(CC(=O)NCCC1=NC(=O)O[N-]1)C(=O)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 13, 22, 34, 47, 47, 47, 121, 121, 201, 201, 201, 201, 201, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 34, 34, 47, 121, 121, 121, 121, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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]) total number of confs: 645 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580516 none CN(CC(=O)NCCC1=NC(=O)O[N-]1)C(=O)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 69, 43, 43, 43, 15, 7, 1, 1, 1, 1, 1, 1, 1, 85, 111, 111, 111, 201, 201, 201, 201, 201, 201, 85, 85, 85, 69, 69, 43, 15, 15, 7, 7, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 853 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580516 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580516 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580516/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580516 Building REAL300025580517 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580517' /scratch/stefan/7787361/working/building/REAL300025580517 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580517 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580517/0 /scratch/stefan/7787361/working/building/REAL300025580517 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/11 `/scratch/stefan/7787361/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC([N+](=O)[O-])=C1C) `REAL300025580517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580517 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC([N+](=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 82, 82, 82, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 19, 19, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 425 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580517 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC([N+](=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 29, 53, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 1, 1, 4, 4, 4, 1, 5, 29, 29, 53, 53, 1, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 16, 17, 18, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580517 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580517 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580517/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580517 Building REAL300025580518 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580518' /scratch/stefan/7787361/working/building/REAL300025580518 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580518 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580518/0 /scratch/stefan/7787361/working/building/REAL300025580518 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/12 `/scratch/stefan/7787361/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCCCN1C(=O)C2=CC=CC=C2C1=O)NCCC1=NC(=O)O[N-]1) `REAL300025580518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580518 none O=C(CCCCCN1C(=O)C2=CC=CC=C2C1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 103, 103, 125, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 12, 6, 1, 1, 1, 1, 1, 1, 1, 103, 103, 125, 125, 125, 125, 125, 125, 198, 198, 201, 201, 201, 201, 32, 12, 12, 6, 6] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 1130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580518 none O=C(CCCCCN1C(=O)C2=CC=CC=C2C1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 8, 9, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 120, 120, 201, 201, 201, 201, 201, 18, 18, 9, 9, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1, 54, 120, 120, 120, 120] 201 rigid atoms, others: [17, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 654 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580518 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580518 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580518/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580518 Building REAL300025580519 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580519' /scratch/stefan/7787361/working/building/REAL300025580519 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580519 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580519/0 /scratch/stefan/7787361/working/building/REAL300025580519 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/13 `/scratch/stefan/7787361/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1=CC=CC=C1) `REAL300025580519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580519 none CC(C)(C)N1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 53, 74, 164, 164, 164, 164, 164, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 53, 53, 74, 74, 1, 1, 1, 1, 1] 164 rigid atoms, others: [41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 462 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580519 none CC(C)(C)N1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 164, 164, 164, 164, 84, 84, 84, 24, 8, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 84, 24, 24, 8, 8, 164, 164, 164, 164, 164] 164 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580519 none CC(C)(C)N1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 13, 13, 13, 53, 74, 164, 164, 164, 164, 164, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 13, 53, 53, 74, 74, 2, 2, 1, 2, 2] 164 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 19, 20] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580519 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580519 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580519/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580519 Building REAL300025580520 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580520' /scratch/stefan/7787361/working/building/REAL300025580520 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580520 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580520/0 /scratch/stefan/7787361/working/building/REAL300025580520 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/14 `/scratch/stefan/7787361/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC=CC=C2N1CCC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580520 none CC1=NC2=CC=CC=C2N1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 60, 60, 60, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 128, 128, 128, 128, 60, 19, 19, 8, 8] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 634 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580520 none CC1=NC2=CC=CC=C2N1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 103, 122, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 19, 105, 105, 122, 122] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580520 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580520 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580520/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580520 Building REAL300025580521 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580521' /scratch/stefan/7787361/working/building/REAL300025580521 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580521 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580521/0 /scratch/stefan/7787361/working/building/REAL300025580521 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/15 `/scratch/stefan/7787361/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(O)=C1) `REAL300025580521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580521 none CCCCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 112, 107, 42, 42, 42, 42, 36, 36, 36, 15, 7, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 201, 201, 201, 201, 201, 201, 201, 112, 112, 42, 42, 36, 15, 15, 7, 7, 84, 42] 402 rigid atoms, others: [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, 40]) total number of confs: 786 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580521 none CCCCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [28, 23, 13, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 42, 42, 42, 42, 42, 1, 1, 1, 28, 28, 28, 28, 28, 23, 23, 13, 13, 1, 1, 4, 12, 12, 12, 12, 2, 1] 402 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 40, 20, 21, 22] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 201 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580521 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580521 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580521/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580521 Building REAL300025580522 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580522' /scratch/stefan/7787361/working/building/REAL300025580522 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580522 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580522/0 /scratch/stefan/7787361/working/building/REAL300025580522 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/16 `/scratch/stefan/7787361/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NN1C1CCCC1) `REAL300025580522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580522 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 5, 5, 5, 37, 37, 37, 98, 98, 179, 179, 179, 179, 179, 5, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 9, 9, 37, 98, 98, 98, 98, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 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]) total number of confs: 508 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580522 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 123, 123, 54, 55, 55, 8, 8, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 179, 179, 179, 179, 150, 150, 150, 150, 150, 54, 8, 8, 8, 8, 123, 179, 179, 179, 179, 179, 179, 179, 179, 179] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 596 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580522 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 10, 10, 10, 47, 47, 123, 123, 123, 123, 123, 1, 1, 1, 1, 5, 5, 5, 5, 3, 3, 3, 2, 2, 10, 47, 47, 47, 47, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 2, 3, 4, 33, 15, 16, 17, 18] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 293 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580522 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580522 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580522/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580522 Building REAL300025580523 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580523' /scratch/stefan/7787361/working/building/REAL300025580523 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580523 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580523/0 /scratch/stefan/7787361/working/building/REAL300025580523 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/17 `/scratch/stefan/7787361/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCS(=O)(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580523 none CCCCS(=O)(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 91, 60, 91, 91, 39, 91, 91, 39, 39, 39, 17, 8, 1, 1, 1, 1, 1, 1, 1, 91, 91, 201, 201, 201, 201, 201, 201, 201, 200, 200, 91, 91, 39, 17, 17, 8, 8, 91, 91] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1026 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580523 none CCCCS(=O)(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 10, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 25, 27, 91, 91, 91, 91, 91, 1, 1, 12, 12, 12, 12, 12, 10, 10, 9, 9, 1, 1, 5, 25, 25, 27, 27, 1, 1] 201 rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 40, 41, 22, 23] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580523 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580523 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580523/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580523 Building REAL300025580524 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580524' /scratch/stefan/7787361/working/building/REAL300025580524 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580524 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580524/0 /scratch/stefan/7787361/working/building/REAL300025580524 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/18 `/scratch/stefan/7787361/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC(F)(F)F)C=N1) `REAL300025580524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580524 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC(F)(F)F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 24, 30, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 1, 1, 6, 24, 24, 30, 30, 1, 1, 10, 10, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580524 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC(F)(F)F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 68, 92, 92, 92, 92, 201, 201, 201, 201, 201, 92, 92, 68, 24, 24, 8, 8, 92, 92, 201, 201, 92] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580524 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580524 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580524/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580524 Building REAL300025580525 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580525' /scratch/stefan/7787361/working/building/REAL300025580525 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580525 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580525/0 /scratch/stefan/7787361/working/building/REAL300025580525 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/19 `/scratch/stefan/7787361/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(=O)N1C) `REAL300025580525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580525 none CC1=C(Br)C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 111, 111, 111, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 111, 24, 24, 8, 8, 201, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 459 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580525 none CC1=C(Br)C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 70, 108, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 13, 70, 70, 108, 108, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 24] set([32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 636 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580525 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580525 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580525/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580525 Building REAL300025580526 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580526' /scratch/stefan/7787361/working/building/REAL300025580526 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580526 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580526/0 /scratch/stefan/7787361/working/building/REAL300025580526 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/20 `/scratch/stefan/7787361/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1)C(F)(F)F) `REAL300025580526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580526 none CC(C)(C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 157, 201, 157, 157, 157, 71, 71, 71, 23, 8, 1, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 157, 71, 23, 23, 8, 8, 157, 157] 201 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, 37, 38]) total number of confs: 611 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580526 none CC(C)(C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 5, 5, 5, 29, 47, 157, 157, 157, 157, 157, 1, 1, 4, 5, 5, 5, 5, 5, 5, 4, 4, 4, 1, 1, 5, 29, 29, 47, 47, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 38, 37, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580526 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580526 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580526/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580526 Building REAL300025580527 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580527' /scratch/stefan/7787361/working/building/REAL300025580527 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580527 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580527/0 /scratch/stefan/7787361/working/building/REAL300025580527 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/21 `/scratch/stefan/7787361/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)CCCCCC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580527 none COC1=CC=C(C(=O)CCCCCC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 179, 201, 201, 179, 97, 179, 80, 88, 80, 68, 21, 21, 21, 9, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 95, 95, 88, 88, 88, 88, 88, 88, 68, 68, 21, 9, 9, 5, 5, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 929 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580527 none COC1=CC=C(C(=O)CCCCCC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 17, 17, 17, 31, 62, 62, 62, 123, 123, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 14, 14, 17, 17, 17, 17, 17, 17, 31, 31, 62, 123, 123, 123, 123, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 46, 47, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580527 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580527 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580527/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580527 Building REAL300025580528 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580528' /scratch/stefan/7787361/working/building/REAL300025580528 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580528 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580528/0 /scratch/stefan/7787361/working/building/REAL300025580528 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/22 `/scratch/stefan/7787361/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=NC2=C1CCC(C(=O)NCCC1=NC(=O)O[N-]1)C2) `REAL300025580528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580528 none CCN1N=NC2=C1CCC(C(=O)NCCC1=NC(=O)O[N-]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 141, 141, 141, 141, 141, 141, 141, 141, 55, 55, 55, 19, 8, 1, 1, 1, 1, 1, 1, 1, 141, 201, 201, 201, 201, 201, 141, 141, 141, 141, 141, 55, 19, 19, 8, 8, 141, 141] 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]) total number of confs: 790 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580528 none CCN1N=NC2=C1CCC(C(=O)NCCC1=NC(=O)O[N-]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 48, 54, 141, 141, 141, 141, 141, 1, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 10, 47, 47, 54, 54, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 38, 37, 21, 27, 28, 29, 30, 31] set([0, 32, 34, 35, 36, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580528 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580528 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580528/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580528 Building REAL300025580529 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580529' /scratch/stefan/7787361/working/building/REAL300025580529 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580529 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580529/0 /scratch/stefan/7787361/working/building/REAL300025580529 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/23 `/scratch/stefan/7787361/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC(F)=CC=C2F)=NO1) `REAL300025580529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580529 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC(F)=CC=C2F)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 38, 38, 110, 119, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 38, 110, 110, 119, 119, 7, 7, 7, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 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]) total number of confs: 583 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580529 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC(F)=CC=C2F)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 54, 64, 183, 183, 183, 183, 183, 1, 1, 1, 1, 7, 7, 8, 7, 7, 7, 8, 1, 1, 11, 54, 54, 64, 64, 1, 1, 1, 8, 7, 8] 201 rigid atoms, others: [1, 11, 12, 13, 14, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 423 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580529 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC(F)=CC=C2F)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 1, 1, 1, 1, 1, 1, 1, 76, 183, 183, 183, 201, 201, 201, 201, 201, 201, 201, 183, 183, 76, 21, 21, 8, 8, 183, 183, 183, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 583 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580529 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580529 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580529/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580529 Building REAL300025580530 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580530' /scratch/stefan/7787361/working/building/REAL300025580530 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580530 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580530/0 /scratch/stefan/7787361/working/building/REAL300025580530 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/24 `/scratch/stefan/7787361/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC(=O)C1=CC=C(Cl)C(Cl)=C1)NCCC1=NC(=O)O[N-]1) `REAL300025580530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580530 none O=C(CCCC(=O)C1=CC=C(Cl)C(Cl)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 1, 1, 1, 1, 16, 1, 16, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 81, 54, 91, 150, 150, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 83, 84, 201, 201, 201, 47, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 826 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580530 none O=C(CCCC(=O)C1=CC=C(Cl)C(Cl)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 1, 1, 1, 1, 16, 1, 16, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 59, 52, 46, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 121, 121, 201, 201, 201, 201, 201, 59, 59, 52, 52, 46, 46, 1, 1, 1, 73, 121, 121, 121, 121] 201 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 650 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580530 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580530 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580530/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580530 Building REAL300025580531 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580531' /scratch/stefan/7787361/working/building/REAL300025580531 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580531 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580531/0 /scratch/stefan/7787361/working/building/REAL300025580531 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/25 `/scratch/stefan/7787361/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC(=O)C1=CC=C2OCCOC2=C1)NCCC1=NC(=O)O[N-]1) `REAL300025580531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580531 none O=C(CCCC(=O)C1=CC=C2OCCOC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 79, 59, 91, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 85, 84, 201, 201, 201, 201, 201, 201, 199, 26, 7, 8, 7, 7] 201 rigid atoms, others: [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: 745 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580531 none O=C(CCCC(=O)C1=CC=C2OCCOC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 30, 24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 113, 113, 201, 201, 201, 201, 201, 40, 40, 30, 30, 24, 24, 1, 1, 1, 1, 1, 1, 1, 76, 113, 113, 113, 113] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 37] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43]) total number of confs: 642 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580531 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580531 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580531/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580531 Building REAL300025580532 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580532' /scratch/stefan/7787361/working/building/REAL300025580532 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580532 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580532/0 /scratch/stefan/7787361/working/building/REAL300025580532 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/26 `/scratch/stefan/7787361/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C(=C1)CCCCC2=O) `REAL300025580532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580532 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C(=C1)CCCCC2=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 36, 53, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 36, 36, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 117 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580532 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C(=C1)CCCCC2=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 20, 8, 1, 1, 1, 1, 1, 1, 1, 51, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 50, 20, 20, 8, 8, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117] 117 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580532 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580532 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580532/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580532 Building REAL300025580533 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580533' /scratch/stefan/7787361/working/building/REAL300025580533 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300025580533 as failed and skipping /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `/scratch/stefan/7787361/failed' `/scratch/stefan/7787361/working/building/REAL300025580533' -> `/scratch/stefan/7787361/failed/REAL300025580533' Building REAL300025580534 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580534' /scratch/stefan/7787361/working/building/REAL300025580534 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580534 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580534/0 /scratch/stefan/7787361/working/building/REAL300025580534 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/27 `/scratch/stefan/7787361/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1CC1=CC=NC=C1) `REAL300025580534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580534 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1CC1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 42, 42, 42, 98, 117, 201, 201, 201, 201, 201, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 42, 97, 98, 117, 117, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 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]) total number of confs: 614 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580534 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1CC1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 58, 58, 58, 19, 7, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 201, 201, 201, 201, 201, 201, 99, 99, 99, 58, 19, 19, 7, 7, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 742 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580534 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1CC1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 37, 44, 99, 99, 99, 99, 99, 1, 1, 1, 1, 4, 6, 6, 5, 6, 6, 2, 2, 2, 9, 37, 37, 44, 44, 4, 4, 6, 6, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17] set([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, 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/7787361/working/building/REAL300025580534 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580534 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580534/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580534 Building REAL300025580535 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580535' /scratch/stefan/7787361/working/building/REAL300025580535 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580535 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580535/0 /scratch/stefan/7787361/working/building/REAL300025580535 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/28 `/scratch/stefan/7787361/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl) `REAL300025580535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580535 none CC1=CC(Br)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 155, 77, 77, 77, 22, 8, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 155, 155, 76, 23, 23, 8, 8, 155] 155 rigid atoms, others: [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]) total number of confs: 368 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580535 none CC1=CC(Br)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 43, 61, 155, 155, 155, 155, 155, 1, 1, 1, 2, 2, 2, 1, 7, 43, 43, 61, 61, 1] 155 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 23, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580535 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580535 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580535/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580535 Building REAL300025580536 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580536' /scratch/stefan/7787361/working/building/REAL300025580536 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580536 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580536/0 /scratch/stefan/7787361/working/building/REAL300025580536 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/29 `/scratch/stefan/7787361/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)C2=CC=C(F)C=C2O1) `REAL300025580536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580536 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)C2=CC=C(F)C=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [12, 1, 12, 12, 59, 68, 154, 154, 154, 154, 154, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 59, 59, 68, 68, 1, 1, 1, 1] 154 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27]) total number of confs: 388 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580536 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)C2=CC=C(F)C=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [62, 62, 23, 8, 1, 1, 1, 1, 1, 1, 1, 62, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 62, 23, 23, 8, 8, 154, 154, 154, 154] 154 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 329 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580536 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580536 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580536/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580536 Building REAL300025580537 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580537' /scratch/stefan/7787361/working/building/REAL300025580537 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580537 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580537/0 /scratch/stefan/7787361/working/building/REAL300025580537 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/30 `/scratch/stefan/7787361/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580537 none COCC(NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 161, 121, 51, 121, 147, 178, 178, 178, 178, 178, 178, 51, 51, 18, 8, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 161, 161, 121, 147, 178, 178, 178, 178, 178, 178, 178, 178, 178, 51, 18, 18, 8, 8] 201 rigid atoms, others: [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: 924 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580537 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580537 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580537/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580537 Building REAL300025580538 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580538' /scratch/stefan/7787361/working/building/REAL300025580538 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580538 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580538/0 /scratch/stefan/7787361/working/building/REAL300025580538 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/31 `/scratch/stefan/7787361/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOC1) `REAL300025580538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580538 none CC(C)(C)OC(=O)NC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 174, 116, 174, 108, 58, 58, 58, 20, 8, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 57, 20, 20, 8, 8, 108, 108, 108, 108, 108, 108] 201 rigid atoms, others: [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, 40, 41, 42, 43, 44]) total number of confs: 655 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580538 none CC(C)(C)OC(=O)NC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 5, 3, 5, 1, 1, 1, 9, 9, 9, 33, 44, 108, 108, 108, 108, 108, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 9, 33, 33, 44, 44, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 7, 8, 9, 41, 39, 44, 40, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 292 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580538 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580538 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580538/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580538 Building REAL300025580539 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580539' /scratch/stefan/7787361/working/building/REAL300025580539 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580539 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580539/0 /scratch/stefan/7787361/working/building/REAL300025580539 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/32 `/scratch/stefan/7787361/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)N2CCC[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580539 none CC1=CC=C(S(=O)(=O)N2CCC[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 160, 160, 84, 160, 160, 84, 84, 84, 84, 49, 84, 49, 49, 19, 8, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 160, 160, 160, 84, 84, 84, 84, 84, 84, 48, 19, 19, 8, 8, 160, 160] 160 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 617 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580539 none CC1=CC=C(S(=O)(=O)N2CCC[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [13, 11, 16, 16, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 34, 84, 84, 84, 84, 84, 16, 16, 17, 17, 17, 16, 16, 1, 1, 1, 1, 1, 1, 6, 25, 25, 34, 34, 16, 16] 160 rigid atoms, others: [32, 33, 34, 35, 36, 5, 8, 9, 10, 11, 12, 13, 14, 37] set([0, 1, 2, 3, 4, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580539 none CC1=CC=C(S(=O)(=O)N2CCC[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 32, 32, 32, 79, 86, 156, 156, 156, 156, 156, 1, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 32, 79, 79, 86, 86, 1, 1] 156 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 44, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 461 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580539 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580539 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580539/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580539 Building REAL300025580540 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580540' /scratch/stefan/7787361/working/building/REAL300025580540 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580540 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580540/0 /scratch/stefan/7787361/working/building/REAL300025580540 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/33 `/scratch/stefan/7787361/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(F)=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1) `REAL300025580540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580540 none N#CC1=CC(F)=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 104, 34, 34, 34, 16, 8, 1, 1, 1, 1, 1, 1, 1, 104, 104, 201, 201, 201, 34, 16, 16, 8, 8, 104, 104, 104, 104, 201] 201 rigid atoms, others: [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: 471 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580540 none N#CC1=CC(F)=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 11, 11, 11, 43, 46, 104, 104, 104, 104, 104, 1, 1, 7, 7, 7, 11, 43, 43, 46, 46, 1, 1, 1, 1, 7] 201 rigid atoms, others: [32, 33, 7, 8, 9, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 267 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580540 none N#CC1=CC(F)=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 35, 35, 35, 105, 107, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 35, 105, 105, 107, 107, 7, 7, 7, 7, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 564 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580540 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580540 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580540/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580540 Building REAL300025580541 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580541' /scratch/stefan/7787361/working/building/REAL300025580541 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580541 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580541/0 /scratch/stefan/7787361/working/building/REAL300025580541 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/34 `/scratch/stefan/7787361/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC(C#N)=C1) `REAL300025580541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580541 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 21, 21, 21, 90, 98, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 21, 90, 90, 98, 98, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 567 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580541 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 22, 66, 22, 22, 7, 3, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 201, 201, 201, 201, 66, 66, 66, 66, 66, 66, 22, 7, 7, 3, 3, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 454 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580541 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580541 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580541/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580541 Building REAL300025580542 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580542' /scratch/stefan/7787361/working/building/REAL300025580542 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580542 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580542/0 /scratch/stefan/7787361/working/building/REAL300025580542 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/35 `/scratch/stefan/7787361/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CN=C1OCC1CC1) `REAL300025580542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580542 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CN=C1OCC1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 8, 1, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 80, 80, 135, 135, 201, 201, 201, 201, 201, 42, 42, 42, 42, 42, 42, 24, 9, 1, 1, 1, 1, 80, 135, 135, 135, 135, 42, 42, 9, 9, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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]) total number of confs: 609 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580542 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CN=C1OCC1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 8, 1, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 38, 38, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 42, 42, 10, 38, 38, 38, 38, 1, 1, 19, 19, 42, 42, 42, 42, 42] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 342 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580542 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CN=C1OCC1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 8, 1, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 1, 1, 1, 1, 1, 1, 1, 40, 94, 94, 94, 94, 94, 94, 94, 131, 152, 201, 201, 40, 15, 15, 7, 7, 94, 94, 152, 152, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 566 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580542 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580542 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580542/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580542 Building REAL300025580543 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580543' /scratch/stefan/7787361/working/building/REAL300025580543 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580543 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580543/0 /scratch/stefan/7787361/working/building/REAL300025580543 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/36 `/scratch/stefan/7787361/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCN(C2=CC=C(Cl)C=C2C#N)CC1) `REAL300025580543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580543 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCN(C2=CC=C(Cl)C=C2C#N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 7, 7, 7, 49, 89, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 7, 49, 49, 89, 89, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 201 rigid atoms, others: [39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 560 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580543 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCN(C2=CC=C(Cl)C=C2C#N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 108, 108, 108, 24, 8, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164, 164, 108, 24, 24, 8, 8, 164, 164, 164, 164, 201, 201, 201, 164, 164, 164, 164] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 611 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580543 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCN(C2=CC=C(Cl)C=C2C#N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 19, 38, 164, 164, 164, 164, 164, 1, 1, 1, 1, 4, 4, 3, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 3, 19, 19, 38, 38, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 42, 43, 44, 13, 14, 15, 16, 45, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580543 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580543 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580543/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580543 Building REAL300025580544 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580544' /scratch/stefan/7787361/working/building/REAL300025580544 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580544 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580544/0 /scratch/stefan/7787361/working/building/REAL300025580544 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/37 `/scratch/stefan/7787361/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580544 none CC(CNC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 82, 135, 165, 193, 193, 201, 201, 201, 201, 34, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 84, 81, 84, 84, 137, 137, 165, 201, 201, 201, 201, 201, 201, 201, 201, 201, 34, 8, 8, 8, 8] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 816 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580544 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580544 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580544/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580544 Building REAL300025580545 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580545' /scratch/stefan/7787361/working/building/REAL300025580545 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580545 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580545/0 /scratch/stefan/7787361/working/building/REAL300025580545 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/38 `/scratch/stefan/7787361/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=CC=CC(Br)=C21) `REAL300025580545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580545 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=CC=CC(Br)=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 29, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 29, 29, 1, 1, 1, 1, 1, 1] 69 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580545 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=CC=CC(Br)=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 21, 7, 1, 1, 1, 1, 1, 1, 1, 67, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 67, 21, 21, 7, 7, 69, 69, 69, 69, 69, 69] 69 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580545 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580545 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580545/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580545 Building REAL300025580546 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580546' /scratch/stefan/7787361/working/building/REAL300025580546 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580546 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580546/0 /scratch/stefan/7787361/working/building/REAL300025580546 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/39 `/scratch/stefan/7787361/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NC(C(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C2)C=C1) `REAL300025580546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580546 none COC1=CC=C(C(=O)NC(C(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 9, 9, 26, 26, 9, 9, 9, 4, 1, 4, 13, 13, 13, 48, 50, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 9, 4, 13, 48, 48, 50, 50, 1, 1, 1, 1, 1, 26, 26] 201 rigid atoms, others: [43, 9, 42, 23, 44, 45, 21, 22, 41, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 406 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580546 none COC1=CC=C(C(=O)NC(C(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 137, 137, 201, 201, 137, 137, 137, 102, 47, 47, 47, 17, 8, 1, 1, 1, 1, 1, 1, 1, 102, 135, 135, 102, 135, 135, 201, 201, 201, 201, 201, 201, 201, 137, 102, 47, 17, 17, 8, 8, 135, 135, 102, 135, 135, 201, 201] 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 1059 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580546 none COC1=CC=C(C(=O)NC(C(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 35, 35, 35, 110, 111, 201, 201, 201, 201, 201, 13, 26, 26, 13, 26, 26, 1, 1, 2, 2, 2, 1, 1, 5, 13, 35, 110, 110, 111, 111, 26, 26, 13, 26, 26, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 46, 47, 33, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 651 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580546 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580546 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580546/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580546 Building REAL300025580547 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580547' /scratch/stefan/7787361/working/building/REAL300025580547 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580547 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580547/0 /scratch/stefan/7787361/working/building/REAL300025580547 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/40 `/scratch/stefan/7787361/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCCCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580547 none NS(=O)(=O)CCCCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 138, 201, 201, 122, 89, 125, 86, 109, 31, 31, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 138, 138, 138, 138, 126, 126, 126, 126, 126, 126, 116, 116, 30, 9, 8, 8, 8] 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]) total number of confs: 1453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580547 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580547 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580547/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580547 Building REAL300025580548 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580548' /scratch/stefan/7787361/working/building/REAL300025580548 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580548 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580548/0 /scratch/stefan/7787361/working/building/REAL300025580548 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/41 `/scratch/stefan/7787361/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C2OC=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1) `REAL300025580548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580548 none CC(C)C1=CC=C2OC=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 200, 200, 84, 84, 84, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 83, 25, 25, 8, 8, 201] 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]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580548 none CC(C)C1=CC=C2OC=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 49, 71, 200, 200, 200, 201, 201, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 9, 48, 48, 71, 71, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 38, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 479 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580548 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580548 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580548/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580548 Building REAL300025580549 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580549' /scratch/stefan/7787361/working/building/REAL300025580549 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580549 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580549/0 /scratch/stefan/7787361/working/building/REAL300025580549 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/42 `/scratch/stefan/7787361/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC3=CC=CN=C32)C=C1) `REAL300025580549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580549 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC3=CC=CN=C32)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 3, 18, 18, 75, 116, 201, 201, 201, 201, 201, 2, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 18, 75, 75, 116, 116, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41]) total number of confs: 642 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580549 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC3=CC=CN=C32)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 31, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 3, 15, 15, 31, 31, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1] 201 rigid atoms, others: [32, 1, 33, 40, 41, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580549 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC3=CC=CN=C32)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 81, 115, 115, 81, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 115, 81, 24, 24, 8, 8, 115, 115, 201, 201, 201, 201, 201, 201, 115, 115] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 600 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580549 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580549 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580549/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580549 Building REAL300025580550 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580550' /scratch/stefan/7787361/working/building/REAL300025580550 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580550 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580550/0 /scratch/stefan/7787361/working/building/REAL300025580550 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/43 `/scratch/stefan/7787361/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(NC(=O)C2CC2)=C1) `REAL300025580550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580550 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(NC(=O)C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 21, 43, 43, 116, 118, 201, 201, 201, 201, 201, 21, 21, 21, 21, 11, 11, 1, 11, 1, 1, 1, 21, 43, 116, 116, 118, 118, 21, 21, 11, 1, 1, 1, 1, 1, 21] 201 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 562 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580550 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(NC(=O)C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 24, 28, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 3, 3, 3, 21, 21, 1, 5, 24, 24, 28, 28, 1, 1, 3, 21, 21, 21, 21, 21, 1] 201 rigid atoms, others: [1, 36, 11, 12, 13, 14, 15, 16, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580550 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(NC(=O)C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 15, 7, 1, 1, 1, 1, 1, 1, 1, 38, 92, 92, 92, 92, 92, 121, 121, 121, 201, 201, 92, 38, 15, 15, 7, 7, 92, 92, 121, 201, 201, 201, 201, 201, 92] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 656 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580550 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580550 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580550/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580550 Building REAL300025580551 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580551' /scratch/stefan/7787361/working/building/REAL300025580551 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580551 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580551/0 /scratch/stefan/7787361/working/building/REAL300025580551 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/44 `/scratch/stefan/7787361/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)(F)F)S1) `REAL300025580551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580551 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 15, 15, 15, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [12, 1, 12, 12, 67, 99, 174, 174, 174, 174, 174, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 66, 66, 99, 99, 1, 1] 174 rigid atoms, others: [1, 11, 12, 13, 14, 15, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 20, 21, 22, 23, 24]) total number of confs: 547 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580551 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 15, 15, 15, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [95, 94, 24, 8, 1, 1, 1, 1, 1, 1, 1, 94, 174, 174, 174, 174, 174, 174, 174, 174, 94, 24, 24, 8, 8, 174, 174] 174 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580551 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580551 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580551/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580551 Building REAL300025580552 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580552' /scratch/stefan/7787361/working/building/REAL300025580552 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580552 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580552/0 /scratch/stefan/7787361/working/building/REAL300025580552 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/45 `/scratch/stefan/7787361/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(=O)NC2=CC=CC=C2)=C1) `REAL300025580552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580552 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(=O)NC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 25, 25, 109, 114, 201, 201, 201, 201, 201, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 25, 109, 109, 114, 114, 9, 9, 9, 3, 1, 1, 1, 1, 1, 9] 201 rigid atoms, others: [35, 36, 37, 38, 39, 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, 40]) total number of confs: 576 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580552 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(=O)NC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 34, 124, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 5, 9, 9, 1, 5, 29, 29, 34, 34, 1, 1, 1, 5, 9, 9, 5, 9, 9, 1] 201 rigid atoms, others: [32, 1, 33, 40, 11, 12, 13, 14, 15, 16, 25, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580552 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(=O)NC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 51, 124, 124, 124, 124, 124, 201, 201, 201, 201, 201, 201, 201, 201, 124, 51, 17, 17, 8, 8, 124, 124, 124, 201, 201, 201, 201, 201, 201, 124] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 543 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580552 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580552 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580552/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580552 Building REAL300025580553 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580553' /scratch/stefan/7787361/working/building/REAL300025580553 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580553 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580553/0 /scratch/stefan/7787361/working/building/REAL300025580553 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/46 `/scratch/stefan/7787361/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)N1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025580553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580553 none CNS(=O)(=O)N1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 161, 201, 201, 161, 161, 161, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 161, 161, 201, 201, 201, 201, 161, 161, 161, 161, 161, 49, 17, 17, 8, 8, 161, 161, 161, 161] 201 rigid atoms, others: [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: 680 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580553 none CNS(=O)(=O)N1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 50, 53, 161, 161, 161, 161, 161, 1, 1, 13, 13, 13, 13, 1, 1, 1, 1, 1, 12, 49, 49, 53, 53, 1, 1, 1, 1] 201 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 39, 38, 20, 21, 26, 27, 28, 29, 30, 37] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 31, 32, 33, 34, 35]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580553 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580553 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580553/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580553 Building REAL300025580554 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580554' /scratch/stefan/7787361/working/building/REAL300025580554 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580554 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580554/0 /scratch/stefan/7787361/working/building/REAL300025580554 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/47 `/scratch/stefan/7787361/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](F)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580554 none CC(C)(C)OC(=O)N1C[C@H](F)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 174, 125, 174, 125, 125, 125, 125, 125, 125, 64, 125, 64, 65, 18, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 125, 64, 18, 18, 7, 7] 201 rigid atoms, others: [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: 654 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580554 none CC(C)(C)OC(=O)N1C[C@H](F)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 11, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 36, 43, 125, 125, 125, 125, 125, 12, 12, 12, 11, 11, 11, 12, 12, 12, 1, 1, 1, 1, 9, 36, 36, 43, 43] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 37] set([0, 1, 2, 3, 4, 6, 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: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580554 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580554 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580554/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580554 Building REAL300025580555 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580555' /scratch/stefan/7787361/working/building/REAL300025580555 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580555 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580555/0 /scratch/stefan/7787361/working/building/REAL300025580555 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/48 `/scratch/stefan/7787361/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C=C1OC)N(C)C(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)=N2) `REAL300025580555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580555 none COC1=CC2=C(C=C1OC)N(C)C(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)=N2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 5, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 144, 144, 144, 144, 144, 144, 144, 144, 201, 144, 144, 144, 144, 36, 36, 36, 19, 8, 1, 1, 1, 1, 1, 1, 1, 144, 201, 201, 201, 144, 144, 201, 201, 201, 144, 144, 144, 36, 19, 19, 8, 8] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 502 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580555 none COC1=CC2=C(C=C1OC)N(C)C(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)=N2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 5, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 55, 144, 144, 144, 144, 144, 1, 4, 4, 4, 1, 1, 4, 4, 4, 2, 2, 2, 9, 50, 50, 55, 55] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 344 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580555 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580555 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580555/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580555 Building REAL300025580556 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580556' /scratch/stefan/7787361/working/building/REAL300025580556 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580556 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580556/0 /scratch/stefan/7787361/working/building/REAL300025580556 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/49 `/scratch/stefan/7787361/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(N2CCC(C(=O)NCCC3=NC(=O)O[N-]3)C2)C(F)=C1) `REAL300025580556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580556 none N#CC1=CC=C(N2CCC(C(=O)NCCC3=NC(=O)O[N-]3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 201, 201, 76, 76, 76, 76, 29, 29, 29, 10, 6, 1, 1, 1, 1, 1, 1, 1, 76, 201, 201, 201, 201, 201, 76, 76, 76, 76, 76, 29, 10, 10, 6, 6, 76, 76, 201] 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]) total number of confs: 403 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580556 none N#CC1=CC=C(N2CCC(C(=O)NCCC3=NC(=O)O[N-]3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 34, 36, 76, 76, 76, 76, 76, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 9, 34, 34, 36, 36, 1, 1, 5] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 38, 37, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 39]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580556 none N#CC1=CC=C(N2CCC(C(=O)NCCC3=NC(=O)O[N-]3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 28, 28, 28, 95, 101, 201, 201, 201, 201, 201, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 28, 95, 95, 101, 101, 5, 5, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 22, 23, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 571 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580556 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580556 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580556/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580556 Building REAL300025580557 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580557' /scratch/stefan/7787361/working/building/REAL300025580557 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580557 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580557/0 /scratch/stefan/7787361/working/building/REAL300025580557 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/50 `/scratch/stefan/7787361/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOCC1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580557 none CC(C)(C)OC(=O)N1CCOCC1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 182, 127, 182, 127, 127, 127, 127, 127, 94, 43, 43, 43, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 127, 127, 127, 94, 94, 43, 19, 19, 8, 8] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 768 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580557 none CC(C)(C)OC(=O)N1CCOCC1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 44, 47, 127, 127, 127, 127, 127, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 44, 44, 47, 47] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580557 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580557 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580557/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580557 Building REAL300025580558 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580558' /scratch/stefan/7787361/working/building/REAL300025580558 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580558 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580558/0 /scratch/stefan/7787361/working/building/REAL300025580558 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/51 `/scratch/stefan/7787361/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(N2CCC(C(=O)NCCC3=NC(=O)O[N-]3)CC2)C(F)=C1) `REAL300025580558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580558 none N#CC1=CC=C(N2CCC(C(=O)NCCC3=NC(=O)O[N-]3)CC2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 147, 147, 147, 147, 62, 62, 62, 20, 8, 1, 1, 1, 1, 1, 1, 1, 147, 147, 201, 201, 201, 201, 201, 147, 147, 147, 147, 147, 61, 21, 21, 8, 8, 147, 147, 147, 147, 201] 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, 41, 42]) total number of confs: 582 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580558 none N#CC1=CC=C(N2CCC(C(=O)NCCC3=NC(=O)O[N-]3)CC2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 57, 74, 147, 147, 147, 147, 147, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 13, 57, 57, 74, 74, 1, 1, 1, 1, 4] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 39, 40, 21, 22, 41, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 42]) total number of confs: 417 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580558 none N#CC1=CC=C(N2CCC(C(=O)NCCC3=NC(=O)O[N-]3)CC2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 32, 32, 32, 99, 114, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 32, 99, 99, 114, 114, 4, 4, 4, 4, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 572 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580558 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580558 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580558/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580558 Building REAL300025580559 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580559' /scratch/stefan/7787361/working/building/REAL300025580559 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580559 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580559/0 /scratch/stefan/7787361/working/building/REAL300025580559 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/52 `/scratch/stefan/7787361/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)C2=CC=CC=C2C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580559 none CN1C(=O)C2=CC=CC=C2C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 93, 93, 93, 23, 8, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 151, 151, 151, 93, 23, 23, 8, 8] 151 rigid atoms, others: [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: 376 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580559 none CN1C(=O)C2=CC=CC=C2C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 53, 79, 151, 151, 151, 151, 151, 2, 2, 2, 1, 1, 1, 1, 1, 10, 53, 53, 79, 79] 151 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 457 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580559 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580559 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580559/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580559 Building REAL300025580560 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580560' /scratch/stefan/7787361/working/building/REAL300025580560 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580560 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580560/0 /scratch/stefan/7787361/working/building/REAL300025580560 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/53 `/scratch/stefan/7787361/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=C(C(F)(F)F)C=C2)N=C1) `REAL300025580560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580560 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=C(C(F)(F)F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 13, 13, 60, 82, 141, 141, 141, 141, 141, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 4, 4, 13, 60, 60, 82, 82, 4, 1, 1, 1, 1, 4] 141 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 430 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580560 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=C(C(F)(F)F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 29, 53, 137, 137, 137, 137, 137, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 4, 4, 4, 1, 1, 5, 29, 29, 53, 53, 1, 4, 4, 4, 4, 1] 141 rigid atoms, others: [1, 36, 11, 12, 13, 14, 24, 25, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 370 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580560 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=C(C(F)(F)F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [69, 69, 23, 8, 1, 1, 1, 1, 1, 1, 1, 69, 137, 137, 137, 141, 141, 137, 137, 141, 141, 141, 141, 141, 137, 137, 68, 23, 23, 8, 8, 137, 141, 141, 141, 141, 137] 141 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580560 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580560 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580560/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580560 Building REAL300025580561 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580561' /scratch/stefan/7787361/working/building/REAL300025580561 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580561 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580561/0 /scratch/stefan/7787361/working/building/REAL300025580561 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/54 `/scratch/stefan/7787361/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C(Cl)N=C12) `REAL300025580561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580561 none CC1=CC=CC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C(Cl)N=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 136, 136, 136, 88, 88, 88, 24, 8, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 88, 24, 24, 8, 8] 136 rigid atoms, others: [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: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580561 none CC1=CC=CC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C(Cl)N=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 41, 71, 136, 136, 136, 136, 136, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 41, 41, 71, 71] 136 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 26, 27, 28, 29] set([32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 30, 31]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580561 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580561 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580561/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580561 Building REAL300025580562 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580562' /scratch/stefan/7787361/working/building/REAL300025580562 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580562 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580562/0 /scratch/stefan/7787361/working/building/REAL300025580562 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/55 `/scratch/stefan/7787361/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1OC) `REAL300025580562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580562 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 136, 136, 136, 136, 51, 51, 51, 17, 8, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 201, 201, 201, 201, 136, 136, 51, 17, 17, 8, 8, 136, 136, 136, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 559 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580562 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 50, 136, 136, 136, 136, 136, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 9, 45, 45, 50, 50, 2, 2, 2, 5, 5, 5] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580562 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580562 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580562/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580562 Building REAL300025580563 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580563' /scratch/stefan/7787361/working/building/REAL300025580563 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580563 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580563/0 /scratch/stefan/7787361/working/building/REAL300025580563 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/56 `/scratch/stefan/7787361/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(C(F)(F)F)C=C1F) `REAL300025580563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580563 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(C(F)(F)F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 78, 123, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 12, 78, 78, 123, 123, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 20, 21, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 659 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580563 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(C(F)(F)F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 24, 24, 8, 8, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580563 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580563 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580563/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580563 Building REAL300025580564 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580564' /scratch/stefan/7787361/working/building/REAL300025580564 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580564 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580564/0 /scratch/stefan/7787361/working/building/REAL300025580564 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/57 `/scratch/stefan/7787361/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC(F)(F)F)C=N1) `REAL300025580564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580564 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC(F)(F)F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 21, 27, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 12, 19, 19, 19, 1, 1, 6, 21, 21, 27, 27, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 20, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580564 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC(F)(F)F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 8, 1, 1, 1, 1, 1, 1, 1, 61, 88, 88, 88, 88, 201, 201, 201, 201, 88, 88, 61, 22, 22, 8, 8, 88, 88, 88] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580564 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580564 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580564/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580564 Building REAL300025580565 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580565' /scratch/stefan/7787361/working/building/REAL300025580565 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580565 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580565/0 /scratch/stefan/7787361/working/building/REAL300025580565 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/58 `/scratch/stefan/7787361/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1) `REAL300025580565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580565 none COC1=CC=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 184, 184, 184, 184, 184, 117, 43, 43, 43, 17, 8, 1, 1, 1, 1, 1, 1, 1, 117, 117, 184, 201, 201, 201, 184, 184, 184, 43, 17, 17, 8, 8, 117, 117, 117, 117, 184] 201 rigid atoms, others: [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]) total number of confs: 515 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580565 none COC1=CC=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 6, 6, 6, 6, 1, 1, 1, 10, 10, 10, 42, 44, 117, 117, 117, 117, 117, 1, 1, 6, 10, 10, 10, 6, 6, 6, 10, 42, 42, 44, 44, 1, 1, 1, 1, 6] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 19, 20] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 273 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580565 none COC1=CC=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 6, 26, 26, 26, 88, 91, 184, 184, 184, 184, 184, 6, 6, 1, 3, 3, 3, 1, 1, 1, 26, 88, 88, 91, 91, 6, 6, 6, 6, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 486 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580565 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580565 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580565/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580565 Building REAL300025580566 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580566' /scratch/stefan/7787361/working/building/REAL300025580566 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580566 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580566/0 /scratch/stefan/7787361/working/building/REAL300025580566 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/59 `/scratch/stefan/7787361/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C2OC=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1) `REAL300025580566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580566 none CCC1=CC=C2OC=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 112, 112, 112, 112, 112, 112, 112, 51, 51, 51, 19, 8, 1, 1, 1, 1, 1, 1, 1, 112, 112, 201, 201, 201, 201, 201, 112, 112, 112, 51, 19, 19, 8, 8, 112] 201 rigid atoms, others: [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]) total number of confs: 796 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580566 none CCC1=CC=C2OC=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 42, 52, 112, 112, 112, 112, 112, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 8, 42, 42, 52, 52, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 20, 21, 27, 28, 29] set([0, 32, 34, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580566 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580566 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580566/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580566 Building REAL300025580567 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580567' /scratch/stefan/7787361/working/building/REAL300025580567 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580567 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580567/0 /scratch/stefan/7787361/working/building/REAL300025580567 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/60 `/scratch/stefan/7787361/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(Br)C(Cl)=C1) `REAL300025580567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580567 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(Br)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 17, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 47, 69, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 47, 47, 69, 69, 1, 1] 153 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 409 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580567 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(Br)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 17, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 20, 8, 1, 1, 1, 1, 1, 1, 1, 57, 153, 153, 153, 153, 153, 153, 153, 153, 57, 20, 20, 8, 8, 153, 153] 153 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580567 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580567 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580567/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580567 Building REAL300025580568 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580568' /scratch/stefan/7787361/working/building/REAL300025580568 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580568 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580568/0 /scratch/stefan/7787361/working/building/REAL300025580568 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/61 `/scratch/stefan/7787361/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN1C=CC2=CC=CC=C21)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580568 none CC(CN1C=CC2=CC=CC=C21)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 43, 110, 146, 201, 201, 201, 201, 201, 201, 201, 201, 43, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 114, 114, 112, 114, 148, 147, 201, 201, 201, 201, 201, 201, 42, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 694 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580568 none CC(CN1C=CC2=CC=CC=C21)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 47, 47, 47, 110, 110, 201, 201, 201, 201, 201, 14, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 47, 110, 110, 110, 110] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 29, 30, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39]) total number of confs: 593 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580568 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580568 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580568/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580568 Building REAL300025580569 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580569' /scratch/stefan/7787361/working/building/REAL300025580569 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580569 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580569/0 /scratch/stefan/7787361/working/building/REAL300025580569 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/62 `/scratch/stefan/7787361/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CC2=NNN=C21) `REAL300025580569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580569 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [12, 1, 12, 12, 60, 72, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 60, 60, 72, 72, 1, 1, 1] 155 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580569 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 83, 155, 155, 155, 155, 155, 155, 155, 155, 155, 83, 24, 24, 8, 8, 155, 155, 155] 155 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580569 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580569 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580569/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580569 Building REAL300025580570 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580570' /scratch/stefan/7787361/working/building/REAL300025580570 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580570 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580570/0 /scratch/stefan/7787361/working/building/REAL300025580570 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/63 `/scratch/stefan/7787361/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOCC(F)(F)C(F)(F)F)NCCC1=NC(=O)O[N-]1) `REAL300025580570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580570 none O=C(CCOCC(F)(F)C(F)(F)F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 5, 15, 15, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 119, 121, 146, 172, 201, 201, 199, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 119, 119, 121, 121, 172, 172, 54, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 814 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580570 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580570 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580570/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580570 Building REAL300025580571 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580571' /scratch/stefan/7787361/working/building/REAL300025580571 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580571 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580571/0 /scratch/stefan/7787361/working/building/REAL300025580571 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/64 `/scratch/stefan/7787361/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1Cl) `REAL300025580571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580571 none NC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1Cl NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 16, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 156, 201, 156, 156, 156, 78, 78, 78, 23, 8, 1, 1, 1, 1, 1, 1, 1, 156, 156, 156, 201, 201, 156, 156, 78, 23, 23, 8, 8] 201 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]) total number of confs: 538 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580571 none NC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1Cl NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 16, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 13, 13, 13, 51, 63, 156, 156, 156, 156, 156, 1, 1, 1, 4, 4, 1, 1, 13, 51, 51, 63, 63] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580571 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580571 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580571/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580571 Building REAL300025580572 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580572' /scratch/stefan/7787361/working/building/REAL300025580572 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580572 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580572/0 /scratch/stefan/7787361/working/building/REAL300025580572 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/65 `/scratch/stefan/7787361/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)(F)F)C=C1N1CCCC1) `REAL300025580572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580572 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)(F)F)C=C1N1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 2, 10, 10, 38, 54, 106, 106, 106, 106, 106, 2, 2, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 38, 38, 54, 54, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1] 106 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 315 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580572 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)(F)F)C=C1N1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 10, 38, 54, 106, 106, 106, 106, 106, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 10, 38, 38, 54, 54, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2] 106 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580572 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)(F)F)C=C1N1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [68, 68, 23, 8, 1, 1, 1, 1, 1, 1, 1, 68, 106, 106, 82, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 68, 23, 23, 8, 8, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106] 106 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580572 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580572 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580572/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580572 Building REAL300025580573 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580573' /scratch/stefan/7787361/working/building/REAL300025580573 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580573 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580573/0 /scratch/stefan/7787361/working/building/REAL300025580573 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/66 `/scratch/stefan/7787361/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC(Br)=CC=C1OCC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580573 none CC(=O)C1=CC(Br)=CC=C1OCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 161, 201, 161, 161, 161, 161, 161, 161, 142, 86, 32, 32, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 161, 161, 161, 94, 94, 31, 8, 8, 8, 8] 201 rigid atoms, others: [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: 609 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580573 none CC(=O)C1=CC(Br)=CC=C1OCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 36, 36, 36, 68, 68, 161, 161, 161, 161, 161, 3, 3, 3, 1, 1, 1, 15, 15, 36, 68, 68, 68, 68] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 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/7787361/working/building/REAL300025580573 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580573 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580573/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580573 Building REAL300025580574 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580574' /scratch/stefan/7787361/working/building/REAL300025580574 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580574 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580574/0 /scratch/stefan/7787361/working/building/REAL300025580574 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/67 `/scratch/stefan/7787361/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(Br)C(=O)N1) `REAL300025580574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580574 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(Br)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 90, 90, 90, 21, 8, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 136, 136, 136, 136, 136, 90, 22, 22, 8, 8, 136, 136] 136 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580574 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(Br)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 40, 64, 136, 136, 136, 136, 136, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 40, 40, 64, 64, 1, 1] 136 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580574 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580574 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580574/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580574 Building REAL300025580575 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580575' /scratch/stefan/7787361/working/building/REAL300025580575 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580575 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580575/0 /scratch/stefan/7787361/working/building/REAL300025580575 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/68 `/scratch/stefan/7787361/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=CC=CC(C(C)C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580575 none CC(C)CC1=CC=CC(C(C)C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 129, 129, 129, 129, 62, 28, 62, 28, 28, 15, 7, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129, 62, 62, 62, 62, 28, 15, 15, 7, 7, 129] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 782 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580575 none CC(C)CC1=CC=CC(C(C)C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 64, 65, 129, 129, 129, 129, 129, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 6, 7, 7, 7, 21, 64, 64, 65, 65, 1] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 44, 22] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580575 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580575 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580575/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580575 Building REAL300025580576 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580576' /scratch/stefan/7787361/working/building/REAL300025580576 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580576 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580576/0 /scratch/stefan/7787361/working/building/REAL300025580576 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/69 `/scratch/stefan/7787361/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCS(=O)(=O)C2=CC=CC=C21) `REAL300025580576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580576 none O=C(NCCC1=NC(=O)O[N-]1)C1CCS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 32, 49, 109, 109, 109, 109, 109, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 32, 32, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1] 109 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580576 none O=C(NCCC1=NC(=O)O[N-]1)C1CCS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 23, 8, 1, 1, 1, 1, 1, 1, 1, 73, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 73, 23, 23, 8, 8, 109, 109, 109, 109, 109, 109, 109, 109, 109] 109 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580576 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580576 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580576/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580576 Building REAL300025580577 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580577' /scratch/stefan/7787361/working/building/REAL300025580577 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580577 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580577/0 /scratch/stefan/7787361/working/building/REAL300025580577 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/70 `/scratch/stefan/7787361/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=CS1) `REAL300025580577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580577 none CC1=NC(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 105, 105, 134, 134, 62, 62, 62, 23, 8, 1, 1, 1, 1, 1, 1, 1, 134, 134, 201, 201, 201, 201, 201, 134, 134, 61, 23, 23, 8, 8, 134, 134, 201] 201 rigid atoms, others: [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]) total number of confs: 571 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580577 none CC1=NC(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 54, 134, 134, 134, 134, 134, 1, 1, 6, 6, 6, 6, 6, 1, 1, 5, 29, 29, 54, 54, 1, 1, 6] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 19, 20, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35]) total number of confs: 357 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580577 none CC1=NC(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 2, 2, 21, 21, 21, 99, 135, 201, 201, 201, 201, 201, 6, 6, 1, 1, 2, 2, 2, 6, 6, 21, 99, 99, 135, 135, 6, 6, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 35, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 694 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580577 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580577 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580577/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580577 Building REAL300025580578 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580578' /scratch/stefan/7787361/working/building/REAL300025580578 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580578 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580578/0 /scratch/stefan/7787361/working/building/REAL300025580578 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/71 `/scratch/stefan/7787361/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NC2=CC=CC=C21) `REAL300025580578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580578 none CN(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 74, 74, 74, 24, 8, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 100, 100, 100, 100, 100, 100, 100, 100, 100, 73, 24, 24, 8, 8, 99, 99, 99, 100] 100 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580578 none CN(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 5, 5, 5, 27, 39, 99, 99, 99, 99, 99, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 3, 3, 3, 1, 5, 27, 27, 39, 39, 1, 1, 1, 1] 100 rigid atoms, others: [1, 3, 4, 5, 6, 39, 17, 18, 19, 20, 21, 22, 23, 36, 38, 30, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580578 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580578 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580578/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580578 Building REAL300025580579 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580579' /scratch/stefan/7787361/working/building/REAL300025580579 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580579 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580579/0 /scratch/stefan/7787361/working/building/REAL300025580579 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/72 `/scratch/stefan/7787361/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=CN1C1CC1) `REAL300025580579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580579 none CC1=CC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=CN1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 100, 111, 201, 201, 201, 201, 201, 4, 1, 1, 1, 1, 4, 4, 4, 4, 32, 100, 100, 111, 111, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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]) total number of confs: 564 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580579 none CC1=CC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=CN1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 147, 147, 76, 76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 147, 147, 147, 201, 201, 147, 147, 147, 147, 75, 24, 24, 8, 8, 147, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 563 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580579 none CC1=CC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=CN1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 61, 147, 147, 147, 147, 147, 1, 1, 1, 4, 4, 1, 1, 1, 1, 12, 50, 50, 61, 61, 1, 4, 4, 4, 4, 4] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 22, 23, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 374 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580579 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580579 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580579/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580579 Building REAL300025580580 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580580' /scratch/stefan/7787361/working/building/REAL300025580580 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580580 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580580/0 /scratch/stefan/7787361/working/building/REAL300025580580 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/73 `/scratch/stefan/7787361/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Br)=C1OC) `REAL300025580580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580580 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Br)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 154, 154, 154, 61, 61, 61, 17, 8, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 154, 201, 201, 201, 201, 154, 61, 17, 17, 8, 8, 154, 201, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 519 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580580 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Br)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 29, 35, 154, 154, 154, 154, 154, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 5, 29, 29, 35, 35, 1, 5, 5, 5] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580580 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580580 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580580/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580580 Building REAL300025580581 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580581' /scratch/stefan/7787361/working/building/REAL300025580581 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580581 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580581/0 /scratch/stefan/7787361/working/building/REAL300025580581 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/74 `/scratch/stefan/7787361/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NC(C2CCCC2)=NC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580581 none NC1=NC(C2CCCC2)=NC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 5, 5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 68, 83, 201, 201, 201, 201, 83, 83, 47, 47, 47, 17, 8, 1, 1, 1, 1, 1, 1, 1, 83, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 47, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 634 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580581 none NC1=NC(C2CCCC2)=NC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 5, 5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 12, 12, 44, 44, 44, 120, 120, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 44, 120, 120, 120, 120] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39]) total number of confs: 563 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580581 none NC1=NC(C2CCCC2)=NC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 5, 5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 1, 1, 8, 8, 8, 31, 34, 83, 83, 83, 83, 83, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 8, 31, 31, 34, 34] 201 rigid atoms, others: [0, 1, 2, 3, 4, 9, 10, 11, 12, 34] set([5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580581 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580581 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580581/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580581 Building REAL300025580582 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580582' /scratch/stefan/7787361/working/building/REAL300025580582 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580582 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580582/0 /scratch/stefan/7787361/working/building/REAL300025580582 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/75 `/scratch/stefan/7787361/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)S(=O)(=O)C1CC1) `REAL300025580582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580582 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)S(=O)(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 16, 16, 48, 48, 48, 104, 113, 201, 201, 201, 201, 201, 1, 5, 5, 1, 1, 1, 16, 16, 16, 16, 16, 16, 48, 104, 104, 113, 113, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 14, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 596 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580582 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)S(=O)(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 60, 165, 60, 60, 20, 8, 1, 1, 1, 1, 1, 1, 1, 165, 177, 177, 177, 201, 201, 165, 165, 165, 165, 165, 165, 60, 20, 21, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 809 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580582 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580582 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580582/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580582 Building REAL300025580583 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580583' /scratch/stefan/7787361/working/building/REAL300025580583 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580583 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580583/0 /scratch/stefan/7787361/working/building/REAL300025580583 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/76 `/scratch/stefan/7787361/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC(C1=NC=CN1)C1=CC=CC=C1)NCCC1=NC(=O)O[N-]1) `REAL300025580583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580583 none O=C(CC(C1=NC=CN1)C1=CC=CC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 140, 180, 201, 201, 201, 201, 180, 199, 199, 181, 199, 199, 8, 8, 1, 1, 1, 1, 1, 1, 1, 145, 145, 180, 201, 201, 201, 199, 199, 199, 199, 199, 54, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 871 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580583 none O=C(CC(C1=NC=CN1)C1=CC=CC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 9, 4, 1, 4, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 44, 44, 118, 118, 199, 199, 199, 199, 199, 9, 9, 4, 11, 11, 11, 1, 1, 1, 1, 1, 44, 118, 118, 118, 118] 201 rigid atoms, others: [32, 33, 34, 3, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39]) total number of confs: 581 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580583 none O=C(CC(C1=NC=CN1)C1=CC=CC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 20, 11, 1, 1, 1, 1, 1, 1, 11, 17, 17, 11, 17, 17, 59, 59, 118, 118, 201, 201, 201, 201, 201, 20, 20, 11, 1, 1, 1, 17, 17, 17, 17, 17, 59, 118, 118, 118, 118] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 27, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 635 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580583 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580583 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580583/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580583 Building REAL300025580584 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580584' /scratch/stefan/7787361/working/building/REAL300025580584 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580584 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580584/0 /scratch/stefan/7787361/working/building/REAL300025580584 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/77 `/scratch/stefan/7787361/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(=O)NCCC1=NC(=O)O[N-]1)C(=O)OC(C)(C)C) `REAL300025580584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580584 none CN(CCC(=O)NCCC1=NC(=O)O[N-]1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 127, 120, 38, 38, 38, 8, 8, 1, 1, 1, 1, 1, 1, 1, 154, 174, 177, 198, 198, 198, 197, 159, 159, 159, 136, 136, 129, 129, 37, 9, 8, 8, 8, 200, 198, 198, 198, 198, 198, 200, 198, 198] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580584 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580584 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580584/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580584 Building REAL300025580585 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580585' /scratch/stefan/7787361/working/building/REAL300025580585 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580585 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580585/0 /scratch/stefan/7787361/working/building/REAL300025580585 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/78 `/scratch/stefan/7787361/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)=NO1) `REAL300025580585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580585 none CC1=CC(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 192, 136, 136, 135, 135, 74, 74, 74, 24, 8, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 201, 201, 201, 201, 192, 192, 73, 24, 24, 8, 8, 136, 136, 136] 201 rigid atoms, others: [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: 655 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580585 none CC1=CC(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 35, 50, 135, 135, 136, 135, 135, 1, 1, 11, 11, 11, 11, 11, 11, 4, 4, 9, 35, 35, 50, 50, 2, 2, 2] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 21] set([0, 1, 2, 3, 10, 11, 12, 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: 364 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580585 none CC1=CC(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 43, 43, 43, 103, 121, 201, 201, 201, 201, 201, 11, 11, 1, 1, 2, 2, 2, 1, 6, 6, 43, 103, 103, 121, 121, 11, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 632 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580585 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580585 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580585/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580585 Building REAL300025580586 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580586' /scratch/stefan/7787361/working/building/REAL300025580586 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580586 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580586/0 /scratch/stefan/7787361/working/building/REAL300025580586 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/79 `/scratch/stefan/7787361/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC=C1Br) `REAL300025580586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580586 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 17, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 43, 71, 177, 177, 177, 177, 177, 1, 1, 1, 1, 1, 1, 7, 43, 43, 71, 71, 1, 1] 177 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) total number of confs: 469 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580586 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 17, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 91, 177, 177, 177, 177, 177, 91, 24, 24, 8, 8, 177, 177] 177 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580586 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580586 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580586/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580586 Building REAL300025580587 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580587' /scratch/stefan/7787361/working/building/REAL300025580587 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580587 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580587/0 /scratch/stefan/7787361/working/building/REAL300025580587 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/80 `/scratch/stefan/7787361/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(Br)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580587 none COC1=CC(C)=C(Br)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 194, 194, 194, 194, 194, 194, 194, 59, 59, 59, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 194, 194, 194, 194, 194, 58, 21, 21, 8, 8] 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]) total number of confs: 402 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580587 none COC1=CC(C)=C(Br)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 70, 81, 194, 194, 194, 194, 194, 4, 4, 4, 1, 2, 2, 2, 1, 12, 70, 70, 81, 81] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 484 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580587 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580587 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580587/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580587 Building REAL300025580588 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580588' /scratch/stefan/7787361/working/building/REAL300025580588 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580588 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580588/0 /scratch/stefan/7787361/working/building/REAL300025580588 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/81 `/scratch/stefan/7787361/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=C1F) `REAL300025580588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580588 none COC1=CC=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 171, 144, 40, 40, 40, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 144, 144, 40, 17, 17, 8, 8] 201 rigid atoms, others: [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: 762 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580588 none COC1=CC=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 3, 5, 25, 25, 25, 81, 83, 201, 201, 201, 201, 201, 1, 1, 3, 3, 3, 1, 1, 1, 3, 3, 5, 5, 25, 81, 81, 83, 83] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 21, 25, 26, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 494 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580588 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580588 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580588/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580588 Building REAL300025580589 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580589' /scratch/stefan/7787361/working/building/REAL300025580589 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580589 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580589/0 /scratch/stefan/7787361/working/building/REAL300025580589 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/82 `/scratch/stefan/7787361/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC(F)=CC(Br)=C2)CC1) `REAL300025580589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580589 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC(F)=CC(Br)=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 15, 1, 1, 17, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 37, 37, 111, 111, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 37, 111, 111, 111, 111, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 555 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580589 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC(F)=CC(Br)=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 15, 1, 1, 17, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 41, 43, 106, 106, 106, 106, 106, 1, 1, 7, 7, 7, 3, 7, 7, 7, 1, 1, 11, 41, 41, 43, 43, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 33, 11, 12, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 274 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580589 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC(F)=CC(Br)=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 15, 1, 1, 17, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 8, 1, 1, 1, 1, 1, 1, 1, 34, 106, 201, 201, 201, 201, 201, 201, 201, 106, 106, 34, 15, 15, 8, 8, 201, 201, 201, 106, 106, 106, 106] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 490 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580589 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580589 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580589/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580589 Building REAL300025580590 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580590' /scratch/stefan/7787361/working/building/REAL300025580590 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580590 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580590/0 /scratch/stefan/7787361/working/building/REAL300025580590 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/83 `/scratch/stefan/7787361/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C1CCC2(CC2C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025580590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580590 none CCC(C)(C)C1CCC2(CC2C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 87, 201, 201, 87, 87, 87, 87, 87, 36, 36, 36, 15, 7, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 87, 87, 87, 87, 87, 87, 87, 36, 15, 15, 7, 7, 87, 87, 87, 87] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 838 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580590 none CCC(C)(C)C1CCC2(CC2C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 31, 87, 87, 87, 87, 87, 1, 1, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 28, 28, 31, 31, 1, 1, 1, 1] 201 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 11, 22, 23, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50, 51] set([0, 1, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580590 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580590 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580590/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580590 Building REAL300025580591 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580591' /scratch/stefan/7787361/working/building/REAL300025580591 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580591 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580591/0 /scratch/stefan/7787361/working/building/REAL300025580591 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/84 `/scratch/stefan/7787361/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CC=CN=C2)=NO1) `REAL300025580591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580591 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CC=CN=C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 28, 28, 28, 99, 107, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 28, 99, 99, 107, 107, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 567 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580591 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CC=CN=C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 47, 47, 19, 8, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 201, 125, 125, 125, 125, 125, 47, 19, 19, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 377 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580591 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CC=CN=C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 10, 47, 57, 125, 125, 125, 125, 125, 1, 1, 11, 11, 11, 11, 11, 1, 1, 2, 2, 2, 10, 46, 46, 57, 57, 11, 11, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 345 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580591 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580591 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580591/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580591 Building REAL300025580592 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580592' /scratch/stefan/7787361/working/building/REAL300025580592 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580592 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580592/0 /scratch/stefan/7787361/working/building/REAL300025580592 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/85 `/scratch/stefan/7787361/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C2N=CSC2=C1)NCCC1=NC(=O)O[N-]1) `REAL300025580592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580592 none O=C(CC1=CC=C2N=CSC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 14, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 98, 201, 201, 201, 201, 201, 201, 201, 201, 15, 8, 1, 1, 1, 1, 1, 1, 1, 98, 98, 201, 201, 201, 201, 40, 15, 15, 8, 8] 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]) total number of confs: 570 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580592 none O=C(CC1=CC=C2N=CSC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 14, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 73, 83, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 17, 73, 73, 83, 83] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 514 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580592 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580592 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580592/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580592 Building REAL300025580593 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580593' /scratch/stefan/7787361/working/building/REAL300025580593 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580593 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580593/0 /scratch/stefan/7787361/working/building/REAL300025580593 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/86 `/scratch/stefan/7787361/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCS(=O)(=O)C1=CC=C(Cl)C=C1)NCCC1=NC(=O)O[N-]1) `REAL300025580593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580593 none O=C(CCCS(=O)(=O)C1=CC=C(Cl)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 95, 73, 99, 201, 201, 201, 201, 201, 201, 201, 201, 201, 13, 8, 1, 1, 1, 1, 1, 1, 1, 95, 95, 99, 99, 99, 99, 201, 201, 201, 201, 39, 13, 13, 8, 8] 201 rigid atoms, others: [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: 1000 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580593 none O=C(CCCS(=O)(=O)C1=CC=C(Cl)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 101, 105, 201, 201, 201, 201, 201, 15, 15, 8, 8, 8, 8, 1, 1, 1, 1, 39, 101, 101, 105, 105] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 603 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580593 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580593 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580593/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580593 Building REAL300025580594 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580594' /scratch/stefan/7787361/working/building/REAL300025580594 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580594 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580594/0 /scratch/stefan/7787361/working/building/REAL300025580594 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/87 `/scratch/stefan/7787361/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=C1)C1=C(C=CC=C1)O2) `REAL300025580594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580594 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=C1)C1=C(C=CC=C1)O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 36, 53, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 36, 36, 53, 53, 1, 1, 1, 1, 1, 1, 1] 103 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580594 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=C1)C1=C(C=CC=C1)O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 23, 8, 1, 1, 1, 1, 1, 1, 1, 54, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 53, 24, 24, 8, 8, 103, 103, 103, 103, 103, 103, 103] 103 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580594 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580594 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580594/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580594 Building REAL300025580595 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580595' /scratch/stefan/7787361/working/building/REAL300025580595 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580595 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580595/0 /scratch/stefan/7787361/working/building/REAL300025580595 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/88 `/scratch/stefan/7787361/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=C3C=CC=NC3=NN2C(C)=C1CCC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580595 none CC1=NC2=C3C=CC=NC3=NN2C(C)=C1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 58, 58, 58, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 149, 149, 57, 19, 19, 8, 8] 201 rigid atoms, others: [21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 660 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580595 none CC1=NC2=C3C=CC=NC3=NN2C(C)=C1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 74, 93, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 19, 76, 76, 93, 93] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 32, 33, 31] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 563 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580595 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580595 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580595/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580595 Building REAL300025580596 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580596' /scratch/stefan/7787361/working/building/REAL300025580596 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580596 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580596/0 /scratch/stefan/7787361/working/building/REAL300025580596 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/89 `/scratch/stefan/7787361/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC1=NC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1[N+](=O)[O-]) `REAL300025580596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580596 none CNC1=NC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 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, 87, 87, 87, 77, 77, 77, 23, 8, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 77, 24, 24, 8, 8] 87 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]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580596 none CNC1=NC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 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: [4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 25, 38, 87, 87, 87, 87, 87, 1, 1, 2, 2, 4, 4, 4, 4, 1, 1, 5, 25, 25, 38, 38] 87 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 18, 19, 26, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580596 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580596 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580596/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580596 Building REAL300025580597 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580597' /scratch/stefan/7787361/working/building/REAL300025580597 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580597 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580597/0 /scratch/stefan/7787361/working/building/REAL300025580597 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/90 `/scratch/stefan/7787361/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](OC1=CC=C(C2=CC=CC=C2)C=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580597 none C[C@H](OC1=CC=C(C2=CC=CC=C2)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 41, 101, 95, 168, 201, 201, 168, 190, 201, 201, 191, 201, 201, 201, 201, 41, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 101, 101, 96, 201, 201, 201, 201, 196, 201, 201, 201, 201, 40, 8, 8, 8, 8] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 756 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580597 none C[C@H](OC1=CC=C(C2=CC=CC=C2)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 9, 24, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 24, 68, 68, 68, 132, 132, 201, 201, 201, 201, 201, 24, 24, 24, 3, 3, 1, 1, 1, 1, 1, 3, 3, 68, 132, 132, 132, 132] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 642 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580597 none C[C@H](OC1=CC=C(C2=CC=CC=C2)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 13, 41, 41, 41, 107, 107, 201, 201, 201, 201, 201, 13, 13, 13, 1, 1, 3, 3, 1, 3, 3, 1, 1, 41, 107, 107, 107, 107] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 14, 15, 38, 37, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 558 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580597 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580597 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580597/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580597 Building REAL300025580598 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580598' /scratch/stefan/7787361/working/building/REAL300025580598 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580598 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580598/0 /scratch/stefan/7787361/working/building/REAL300025580598 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/91 `/scratch/stefan/7787361/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2OC(=S)[N-]C2=C1) `REAL300025580598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580598 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2OC(=S)[N-]C2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'S.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 14, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 3, 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: [5, 1, 5, 5, 30, 44, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 30, 30, 44, 44, 1, 1, 1] 86 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580598 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2OC(=S)[N-]C2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'S.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 14, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 3, 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: [44, 44, 24, 8, 1, 1, 1, 1, 1, 1, 1, 44, 86, 86, 86, 86, 86, 86, 86, 86, 86, 43, 24, 24, 8, 8, 86, 86, 86] 86 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580598 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580598 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580598/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580598 Building REAL300025580599 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580599' /scratch/stefan/7787361/working/building/REAL300025580599 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580599 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580599/0 /scratch/stefan/7787361/working/building/REAL300025580599 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/92 `/scratch/stefan/7787361/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C=C([N+](=O)[O-])C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580599 none CC1=C(Br)C=C([N+](=O)[O-])C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 8, 11, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 144, 201, 201, 201, 201, 201, 81, 81, 81, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 81, 23, 23, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 663 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580599 none CC1=C(Br)C=C([N+](=O)[O-])C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 8, 11, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 57, 93, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 9, 57, 57, 93, 93] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 571 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580599 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580599 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580599/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580599 Building REAL300025580600 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580600' /scratch/stefan/7787361/working/building/REAL300025580600 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580600 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580600/0 /scratch/stefan/7787361/working/building/REAL300025580600 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/93 `/scratch/stefan/7787361/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=C1Br) `REAL300025580600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580600 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 49, 49, 49, 20, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131, 131, 49, 21, 21, 8, 8, 131] 131 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]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580600 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 7, 7, 7, 41, 61, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 2, 2, 2, 1, 7, 41, 41, 61, 61, 1] 131 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 23, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580600 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580600 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580600/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580600 Building REAL300025580601 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580601' /scratch/stefan/7787361/working/building/REAL300025580601 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580601 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580601/0 /scratch/stefan/7787361/working/building/REAL300025580601 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/94 `/scratch/stefan/7787361/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC1=CC=C(C(F)(F)F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580601 none CCC(CC1=CC=C(C(F)(F)F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 141, 64, 141, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 64, 64, 19, 8, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 160, 141, 201, 201, 201, 201, 201, 201, 64, 19, 19, 8, 8] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1058 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580601 none CCC(CC1=CC=C(C(F)(F)F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 19, 19, 19, 82, 96, 201, 201, 201, 201, 201, 7, 7, 7, 7, 7, 5, 2, 2, 1, 1, 1, 1, 19, 82, 82, 96, 96] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 12, 13, 35, 36] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580601 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580601 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580601/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580601 Building REAL300025580602 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580602' /scratch/stefan/7787361/working/building/REAL300025580602 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580602 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580602/0 /scratch/stefan/7787361/working/building/REAL300025580602 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/95 `/scratch/stefan/7787361/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2)C=C1[O-]) `REAL300025580602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580602 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2)C=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [9, 7, 9, 9, 17, 17, 51, 51, 51, 51, 51, 6, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 9, 17, 17, 17, 17, 1, 1, 1, 1, 7] 51 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 105 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580602 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2)C=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [4, 1, 4, 4, 12, 12, 33, 33, 33, 33, 33, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 1, 4, 12, 12, 12, 12, 7, 7, 6, 7, 1] 51 rigid atoms, others: [1, 33, 11, 12, 13, 14, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580602 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2)C=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 33, 33, 33, 51, 51, 51, 51, 51, 51, 33, 33, 33, 14, 4, 4, 4, 4, 51, 51, 51, 51, 33] 51 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580602 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580602 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580602/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580602 Building REAL300025580603 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580603' /scratch/stefan/7787361/working/building/REAL300025580603 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580603 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580603/0 /scratch/stefan/7787361/working/building/REAL300025580603 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/96 `/scratch/stefan/7787361/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C)C=CN=C2C(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580603 none CC1=CC2=C(C)C=CN=C2C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 89, 89, 89, 23, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 89, 24, 24, 8, 8, 165] 165 rigid atoms, others: [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: 399 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580603 none CC1=CC2=C(C)C=CN=C2C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 59, 89, 165, 165, 165, 165, 165, 1, 2, 2, 2, 1, 2, 2, 2, 1, 1, 12, 59, 59, 89, 89, 1] 165 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 26, 37, 30, 31] set([32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29]) total number of confs: 512 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580603 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580603 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580603/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580603 Building REAL300025580604 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580604' /scratch/stefan/7787361/working/building/REAL300025580604 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580604 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580604/0 /scratch/stefan/7787361/working/building/REAL300025580604 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/97 `/scratch/stefan/7787361/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2CCCCC2)=N1) `REAL300025580604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580604 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 5, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 12, 28, 28, 84, 112, 201, 201, 201, 201, 201, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 28, 84, 84, 112, 112, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 591 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580604 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 5, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 22, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 4, 16, 16, 22, 22, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 21, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580604 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 5, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 65, 72, 72, 72, 72, 201, 201, 201, 201, 201, 72, 65, 24, 24, 8, 8, 72, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 587 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580604 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580604 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580604/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580604 Building REAL300025580605 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580605' /scratch/stefan/7787361/working/building/REAL300025580605 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580605 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580605/0 /scratch/stefan/7787361/working/building/REAL300025580605 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/98 `/scratch/stefan/7787361/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN2C=CC(Cl)=CC2=C1) `REAL300025580605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580605 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN2C=CC(Cl)=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 12, 56, 77, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 56, 56, 77, 77, 1, 1, 1, 1] 118 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580605 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN2C=CC(Cl)=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [74, 74, 21, 8, 1, 1, 1, 1, 1, 1, 1, 74, 117, 117, 117, 117, 118, 118, 118, 118, 118, 73, 21, 21, 8, 8, 117, 117, 118, 118] 118 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580605 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580605 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580605/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580605 Building REAL300025580606 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580606' /scratch/stefan/7787361/working/building/REAL300025580606 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580606 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580606/0 /scratch/stefan/7787361/working/building/REAL300025580606 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/99 `/scratch/stefan/7787361/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(OC2=CC=C(Cl)C=C2)CC1) `REAL300025580606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580606 none O=C(NCCC1=NC(=O)O[N-]1)C1(OC2=CC=C(Cl)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 39, 39, 114, 115, 201, 201, 201, 201, 201, 6, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 39, 114, 114, 115, 115, 1, 1, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 582 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580606 none O=C(NCCC1=NC(=O)O[N-]1)C1(OC2=CC=C(Cl)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 43, 47, 119, 119, 119, 119, 119, 1, 1, 7, 15, 15, 10, 10, 15, 15, 1, 1, 9, 43, 43, 47, 47, 15, 15, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 11, 12, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580606 none O=C(NCCC1=NC(=O)O[N-]1)C1(OC2=CC=C(Cl)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 1, 1, 1, 1, 1, 1, 1, 41, 119, 194, 201, 201, 201, 201, 201, 201, 119, 119, 41, 15, 15, 7, 7, 201, 201, 201, 201, 119, 119, 119, 119] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580606 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580606 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580606/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580606 Building REAL300025580607 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580607' /scratch/stefan/7787361/working/building/REAL300025580607 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580607 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580607/0 /scratch/stefan/7787361/working/building/REAL300025580607 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/100 `/scratch/stefan/7787361/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC(=O)C2=CC=CC=C21) `REAL300025580607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580607 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC(=O)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 31, 49, 118, 118, 118, 118, 118, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 31, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1] 118 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 317 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580607 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC(=O)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 77, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 77, 24, 24, 8, 8, 118, 118, 118, 118, 118, 118, 118, 118, 118] 118 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 385 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580607 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580607 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580607/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580607 Building REAL300025580608 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580608' /scratch/stefan/7787361/working/building/REAL300025580608 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580608 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580608/0 /scratch/stefan/7787361/working/building/REAL300025580608 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/101 `/scratch/stefan/7787361/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC(F)=C1Br) `REAL300025580608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580608 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC(F)=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 15, 1, 17, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 40, 62, 154, 154, 154, 154, 154, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 40, 40, 62, 62, 1, 1] 154 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580608 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC(F)=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 15, 1, 17, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 20, 8, 1, 1, 1, 1, 1, 1, 1, 79, 154, 154, 154, 147, 154, 154, 154, 154, 79, 21, 21, 8, 8, 154, 154] 154 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580608 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580608 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580608/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580608 Building REAL300025580609 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580609' /scratch/stefan/7787361/working/building/REAL300025580609 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580609 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580609/0 /scratch/stefan/7787361/working/building/REAL300025580609 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/102 `/scratch/stefan/7787361/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(=O)C=C1C) `REAL300025580609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580609 none COCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(=O)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 189, 123, 123, 123, 63, 63, 63, 18, 8, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 201, 201, 201, 201, 201, 189, 189, 123, 62, 18, 18, 8, 8, 123, 123, 123, 123] 201 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, 37, 38, 39]) total number of confs: 753 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580609 none COCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(=O)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 2, 1, 1, 1, 1, 1, 12, 12, 12, 32, 44, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 11, 11, 11, 5, 5, 2, 2, 1, 12, 32, 32, 44, 44, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 39, 18, 19, 20, 21, 22, 36, 38, 30, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580609 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580609 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580609/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580609 Building REAL300025580610 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580610' /scratch/stefan/7787361/working/building/REAL300025580610 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025580610 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580610/0 /scratch/stefan/7787361/working/building/REAL300025580610 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/103 `/scratch/stefan/7787361/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC([NH+]2CCC(C(=O)NCCC3=NC(=O)O[N-]3)CC2)CC1) `REAL300025580610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580610 none CCN1CCC([NH+]2CCC(C(=O)NCCC3=NC(=O)O[N-]3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 124, 124, 124, 124, 124, 53, 53, 53, 16, 8, 1, 1, 1, 1, 1, 1, 1, 124, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124, 124, 124, 124, 53, 16, 16, 8, 8, 124, 124, 124, 124, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 634 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580610 none CCN1CCC([NH+]2CCC(C(=O)NCCC3=NC(=O)O[N-]3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 33, 40, 124, 124, 124, 124, 124, 1, 1, 5, 5, 13, 13, 13, 13, 13, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 33, 33, 40, 40, 1, 1, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [11, 36, 5, 6, 7, 8, 9, 10, 39, 46, 47, 48, 40, 22, 23, 49, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 314 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580610 none CCN1CCC([NH+]2CCC(C(=O)NCCC3=NC(=O)O[N-]3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 25, 25, 25, 78, 88, 201, 201, 201, 201, 201, 5, 5, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 25, 78, 78, 88, 88, 5, 5, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 50, 35, 52, 53, 24, 25, 51, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 517 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580610 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025580610/1 /scratch/stefan/7787361/working/building/REAL300025580610 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/104 `/scratch/stefan/7787361/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+]1CCC([NH+]2CCC(C(=O)NCCC3=NC(=O)O[N-]3)CC2)CC1) `REAL300025580610.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025580610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580610 none CC[NH+]1CCC([NH+]2CCC(C(=O)NCCC3=NC(=O)O[N-]3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 137, 68, 68, 68, 17, 8, 1, 1, 1, 1, 1, 1, 1, 137, 137, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 137, 68, 17, 17, 8, 8, 137, 137, 137, 137, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 628 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580610 none CC[NH+]1CCC([NH+]2CCC(C(=O)NCCC3=NC(=O)O[N-]3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 38, 47, 137, 137, 137, 137, 137, 1, 1, 6, 6, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 9, 38, 38, 47, 47, 1, 1, 1, 1, 6, 6, 6, 6] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 47, 48, 40, 50, 41, 23, 24, 39, 49, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 51, 52, 53, 54]) total number of confs: 355 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580610 none CC[NH+]1CCC([NH+]2CCC(C(=O)NCCC3=NC(=O)O[N-]3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 23, 23, 23, 75, 86, 201, 201, 201, 201, 201, 6, 6, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 23, 75, 75, 86, 86, 6, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 52, 53, 54, 25, 26, 51, 36] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 512 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580610 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580610 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025580610/1.* 0: /scratch/stefan/7787361/working/building/REAL300025580610/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580610 Building REAL300025580611 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580611' /scratch/stefan/7787361/working/building/REAL300025580611 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580611 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580611/0 /scratch/stefan/7787361/working/building/REAL300025580611 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/105 `/scratch/stefan/7787361/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(=O)NCCC1=NC(=O)O[N-]1)CC1=CC=CC=C1Cl) `REAL300025580611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580611 none CCN(CC(=O)NCCC1=NC(=O)O[N-]1)CC1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 5, 7, 12, 28, 28, 28, 100, 105, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 12, 12, 28, 100, 100, 105, 105, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 605 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580611 none CCN(CC(=O)NCCC1=NC(=O)O[N-]1)CC1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 167, 124, 43, 43, 43, 18, 8, 1, 1, 1, 1, 1, 1, 1, 167, 173, 201, 201, 201, 201, 201, 201, 171, 171, 171, 171, 171, 124, 124, 43, 18, 18, 8, 8, 173, 173, 201, 201, 201, 201] 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, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 761 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580611 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580611 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580611/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580611 Building REAL300025580612 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580612' /scratch/stefan/7787361/working/building/REAL300025580612 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580612 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580612/0 /scratch/stefan/7787361/working/building/REAL300025580612 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/106 `/scratch/stefan/7787361/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCN(CC(F)(F)F)CC1) `REAL300025580612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580612 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(CC(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 54, 64, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 12, 54, 54, 64, 64, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 11, 12, 13, 14, 15, 20, 21, 27, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 16, 17, 18, 19, 22, 23, 24, 25, 26]) total number of confs: 348 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580612 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(CC(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 19, 8, 1, 1, 1, 1, 1, 1, 1, 63, 125, 125, 125, 125, 201, 201, 201, 201, 125, 125, 63, 19, 19, 8, 8, 125, 125, 125, 125, 125, 201, 201, 125, 125, 125, 125] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 858 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580612 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580612 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580612/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580612 Building REAL300025580613 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580613' /scratch/stefan/7787361/working/building/REAL300025580613 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580613 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580613/0 /scratch/stefan/7787361/working/building/REAL300025580613 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/107 `/scratch/stefan/7787361/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580613 none CS(=O)(=O)C1=CC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 201, 201, 183, 183, 162, 183, 183, 162, 68, 68, 68, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 183, 162, 183, 183, 162, 162, 67, 20, 21, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 875 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580613 none CS(=O)(=O)C1=CC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 55, 70, 183, 183, 183, 183, 183, 5, 5, 5, 1, 1, 1, 1, 4, 4, 12, 55, 55, 70, 70] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 472 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580613 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580613 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580613/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580613 Building REAL300025580614 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580614' /scratch/stefan/7787361/working/building/REAL300025580614 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580614 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580614/0 /scratch/stefan/7787361/working/building/REAL300025580614 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/108 `/scratch/stefan/7787361/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(CC2=CC=CC=C2)=NN1) `REAL300025580614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580614 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(CC2=CC=CC=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 17, 37, 37, 105, 109, 201, 201, 201, 201, 201, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 17, 17, 37, 105, 105, 109, 109, 17, 3, 3, 1, 1, 1, 1, 1, 17] 201 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 31] 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, 36]) total number of confs: 538 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580614 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(CC2=CC=CC=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 23, 24, 78, 78, 78, 78, 78, 1, 1, 1, 1, 9, 17, 17, 13, 17, 17, 1, 1, 7, 22, 22, 24, 24, 1, 9, 9, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [1, 36, 11, 12, 13, 14, 21, 22, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580614 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(CC2=CC=CC=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 17, 8, 1, 1, 1, 1, 1, 1, 1, 43, 78, 78, 78, 195, 201, 201, 201, 201, 201, 78, 78, 43, 17, 17, 8, 8, 78, 195, 195, 201, 201, 201, 201, 201, 78] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580614 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580614 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580614/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580614 Building REAL300025580615 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580615' /scratch/stefan/7787361/working/building/REAL300025580615 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025580615 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580615/0 /scratch/stefan/7787361/working/building/REAL300025580615 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/109 `/scratch/stefan/7787361/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C=NC2=CC=C(Cl)C=C21) `REAL300025580615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580615 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C=NC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 8, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 356 conformations in input total number of sets (complete confs): 356 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 49, 84, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 49, 49, 84, 84, 2, 1, 1, 1, 1] 356 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28]) total number of confs: 508 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580615 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C=NC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 8, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 356 conformations in input total number of sets (complete confs): 356 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 24, 8, 1, 1, 1, 1, 1, 1, 1, 92, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 91, 24, 24, 8, 8, 356, 178, 178, 178, 178] 356 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 767 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580615 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025580615/1 /scratch/stefan/7787361/working/building/REAL300025580615 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/110 `/scratch/stefan/7787361/working/3D/110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C([O-])C=NC2=CC=C(Cl)C=C21) `REAL300025580615.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025580615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580615 none O=C(NCCC1=NC(=O)O[N-]1)C1=C([O-])C=NC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 8, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 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: [6, 1, 6, 6, 24, 25, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 25, 25, 1, 1, 1, 1] 61 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580615 none O=C(NCCC1=NC(=O)O[N-]1)C1=C([O-])C=NC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 8, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 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: [49, 49, 14, 8, 1, 1, 1, 1, 1, 1, 1, 49, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 48, 14, 14, 8, 8, 61, 61, 61, 61] 61 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580615 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580615 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025580615/1.* 0: /scratch/stefan/7787361/working/building/REAL300025580615/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580615 Building REAL300025580616 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580616' /scratch/stefan/7787361/working/building/REAL300025580616 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580616 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580616/0 /scratch/stefan/7787361/working/building/REAL300025580616 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/111 `/scratch/stefan/7787361/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025580616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580616 none CCOC(=O)C1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 192, 192, 131, 192, 131, 132, 132, 72, 73, 73, 24, 8, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 201, 200, 200, 132, 72, 24, 24, 8, 8] 201 rigid atoms, others: [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: 623 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580616 none CCOC(=O)C1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 30, 37, 131, 131, 131, 131, 131, 1, 19, 19, 19, 18, 18, 1, 6, 30, 30, 37, 37] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 20, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580616 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580616 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580616/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580616 Building REAL300025580617 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580617' /scratch/stefan/7787361/working/building/REAL300025580617 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580617 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580617/0 /scratch/stefan/7787361/working/building/REAL300025580617 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/112 `/scratch/stefan/7787361/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F) `REAL300025580617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580617 none CS(=O)(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 201, 201, 163, 163, 66, 66, 66, 17, 8, 1, 1, 1, 1, 1, 1, 1, 163, 163, 66, 66, 201, 201, 201, 163, 66, 17, 17, 8, 8, 163, 163] 201 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]) total number of confs: 787 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580617 none CS(=O)(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 1, 1, 1, 1, 5, 5, 5, 29, 40, 163, 163, 163, 163, 163, 1, 1, 1, 1, 7, 7, 7, 1, 5, 29, 29, 40, 40, 1, 1] 201 rigid atoms, others: [32, 1, 4, 5, 6, 7, 18, 19, 20, 21, 25, 31] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580617 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580617 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580617/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580617 Building REAL300025580618 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580618' /scratch/stefan/7787361/working/building/REAL300025580618 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580618 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580618/0 /scratch/stefan/7787361/working/building/REAL300025580618 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/113 `/scratch/stefan/7787361/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(Br)C(F)=CC=C2N1) `REAL300025580618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580618 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(Br)C(F)=CC=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 54, 73, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 53, 53, 73, 73, 1, 1, 1, 1] 116 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 366 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580618 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(Br)C(F)=CC=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 23, 8, 1, 1, 1, 1, 1, 1, 1, 69, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 69, 23, 23, 8, 8, 116, 116, 116, 116] 116 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580618 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580618 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580618/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580618 Building REAL300025580619 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580619' /scratch/stefan/7787361/working/building/REAL300025580619 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580619 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580619/0 /scratch/stefan/7787361/working/building/REAL300025580619 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/114 `/scratch/stefan/7787361/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N[C@@H](CC(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580619 none COC(=O)N[C@@H](CC(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 150, 198, 121, 36, 121, 121, 133, 133, 133, 37, 37, 8, 8, 1, 1, 1, 1, 1, 1, 1, 198, 198, 198, 150, 133, 133, 133, 133, 133, 133, 133, 133, 133, 36, 9, 9, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 817 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580619 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580619 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580619/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580619 Building REAL300025580620 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580620' /scratch/stefan/7787361/working/building/REAL300025580620 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580620 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580620/0 /scratch/stefan/7787361/working/building/REAL300025580620 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/115 `/scratch/stefan/7787361/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2CCC1C(C(=O)NCCC1=NC(=O)O[N-]1)C2) `REAL300025580620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580620 none CC(C)(C)OC(=O)N1CC2CCC1C(C(=O)NCCC1=NC(=O)O[N-]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 181, 133, 181, 133, 133, 133, 133, 133, 133, 67, 67, 67, 21, 8, 1, 1, 1, 1, 1, 1, 1, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 133, 133, 133, 133, 133, 133, 133, 133, 66, 21, 21, 8, 8, 133, 133] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 651 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580620 none CC(C)(C)OC(=O)N1CC2CCC1C(C(=O)NCCC1=NC(=O)O[N-]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 44, 56, 133, 133, 133, 133, 133, 1, 11, 11, 11, 10, 10, 10, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 43, 43, 56, 56, 1, 1] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 50, 43, 41, 25, 49, 42, 39, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 369 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580620 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580620 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580620/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580620 Building REAL300025580621 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580621' /scratch/stefan/7787361/working/building/REAL300025580621 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580621 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580621/0 /scratch/stefan/7787361/working/building/REAL300025580621 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/116 `/scratch/stefan/7787361/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(SCC2CC2)=C1F) `REAL300025580621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580621 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(SCC2CC2)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 14, 5, 5, 5, 5, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 16, 52, 52, 108, 109, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 11, 4, 1, 1, 1, 1, 16, 16, 52, 108, 108, 109, 109, 16, 16, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 564 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580621 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(SCC2CC2)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 14, 5, 5, 5, 5, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 25, 28, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 5, 10, 16, 16, 1, 1, 7, 25, 25, 28, 28, 1, 1, 10, 10, 16, 16, 16, 16, 16] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 22, 23, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580621 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(SCC2CC2)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 14, 5, 5, 5, 5, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 12, 7, 1, 1, 1, 1, 1, 1, 1, 25, 59, 59, 59, 59, 59, 59, 81, 143, 201, 201, 59, 59, 25, 12, 12, 7, 7, 59, 59, 143, 143, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580621 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580621 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580621/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580621 Building REAL300025580622 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580622' /scratch/stefan/7787361/working/building/REAL300025580622 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580622 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580622/0 /scratch/stefan/7787361/working/building/REAL300025580622 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/117 `/scratch/stefan/7787361/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1) `REAL300025580622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580622 none CC(C)(C)OC(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 178, 139, 178, 50, 50, 50, 50, 34, 34, 34, 15, 7, 1, 1, 1, 1, 1, 1, 1, 50, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 50, 50, 34, 15, 15, 7, 7, 50] 201 rigid atoms, others: [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]) total number of confs: 615 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580622 none CC(C)(C)OC(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 17, 17, 9, 5, 9, 1, 1, 1, 1, 1, 1, 3, 3, 4, 17, 18, 50, 50, 50, 50, 50, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 4, 17, 17, 18, 18, 1] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580622 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580622 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580622/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580622 Building REAL300025580623 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580623' /scratch/stefan/7787361/working/building/REAL300025580623 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580623 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580623/0 /scratch/stefan/7787361/working/building/REAL300025580623 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/118 `/scratch/stefan/7787361/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=C(Cl)C=C2)C=N1) `REAL300025580623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580623 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=C(Cl)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 23, 23, 83, 99, 201, 201, 201, 201, 201, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 23, 83, 83, 99, 99, 11, 11, 1, 1, 1, 1, 11] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 556 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580623 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=C(Cl)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 4, 17, 21, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 9, 11, 11, 11, 11, 11, 11, 1, 1, 4, 17, 17, 21, 21, 1, 1, 11, 11, 11, 11, 1] 201 rigid atoms, others: [1, 36, 11, 12, 13, 14, 15, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580623 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=C(Cl)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 8, 1, 1, 1, 1, 1, 1, 1, 47, 66, 66, 66, 66, 197, 201, 201, 201, 201, 201, 201, 66, 66, 47, 18, 18, 8, 8, 66, 66, 201, 201, 201, 201, 66] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580623 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580623 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580623/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580623 Building REAL300025580624 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580624' /scratch/stefan/7787361/working/building/REAL300025580624 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580624 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580624/0 /scratch/stefan/7787361/working/building/REAL300025580624 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/119 `/scratch/stefan/7787361/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1) `REAL300025580624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580624 none COC1=CC=CC=C1OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 160, 57, 57, 57, 57, 44, 44, 44, 13, 7, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 201, 201, 57, 57, 44, 13, 13, 7, 7, 57] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 383 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580624 none COC1=CC=CC=C1OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 18, 18, 18, 16, 18, 18, 8, 1, 1, 1, 1, 1, 1, 3, 3, 4, 16, 22, 57, 57, 57, 57, 57, 1, 1, 26, 26, 26, 18, 18, 18, 18, 1, 1, 4, 16, 16, 22, 22, 1] 201 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580624 none COC1=CC=CC=C1OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 18, 26, 26, 26, 74, 93, 201, 201, 201, 201, 201, 18, 18, 4, 4, 4, 1, 1, 1, 1, 18, 18, 26, 74, 74, 93, 93, 18] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 560 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580624 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580624 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580624/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580624 Building REAL300025580625 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580625' /scratch/stefan/7787361/working/building/REAL300025580625 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580625 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580625/0 /scratch/stefan/7787361/working/building/REAL300025580625 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/120 `/scratch/stefan/7787361/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=C(C=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)C(=O)N(C)C1=O) `REAL300025580625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580625 none CN1C2=C(C=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)C(=O)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 6, 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: [141, 141, 141, 141, 141, 78, 78, 78, 22, 8, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 141, 141, 141, 142, 142, 142, 142, 77, 22, 22, 8, 8, 142, 142, 142] 142 rigid atoms, others: [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]) total number of confs: 364 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580625 none CN1C2=C(C=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)C(=O)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 61, 81, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 60, 60, 81, 81, 2, 2, 2] 142 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 27] set([32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580625 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580625 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580625/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580625 Building REAL300025580626 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580626' /scratch/stefan/7787361/working/building/REAL300025580626 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580626 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580626/0 /scratch/stefan/7787361/working/building/REAL300025580626 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/121 `/scratch/stefan/7787361/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(N2CCOCC2)C(F)=C1) `REAL300025580626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580626 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(N2CCOCC2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [14, 1, 14, 14, 57, 84, 153, 153, 153, 153, 153, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 57, 57, 84, 84, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4] 153 rigid atoms, others: [32, 34, 35, 36, 37, 38, 33, 15, 16, 17, 18, 19, 20, 21, 31] 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, 39]) total number of confs: 462 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580626 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(N2CCOCC2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 45, 72, 149, 149, 149, 149, 149, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 7, 45, 45, 72, 72, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1] 153 rigid atoms, others: [1, 39, 11, 12, 13, 14, 15, 16, 22, 23, 24, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 420 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580626 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(N2CCOCC2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 91, 149, 149, 149, 116, 149, 153, 153, 153, 153, 153, 149, 149, 149, 90, 24, 24, 8, 8, 149, 153, 153, 153, 153, 153, 153, 153, 153, 149] 153 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 554 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580626 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580626 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580626/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580626 Building REAL300025580627 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580627' /scratch/stefan/7787361/working/building/REAL300025580627 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580627 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580627/0 /scratch/stefan/7787361/working/building/REAL300025580627 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/122 `/scratch/stefan/7787361/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)C=C1) `REAL300025580627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580627 none COC1=CC=C(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 168, 168, 201, 201, 168, 44, 44, 44, 44, 39, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 44, 44, 201, 201, 201, 201, 201, 201, 201, 44, 44, 39, 8, 9, 8, 8, 44, 201, 201] 201 rigid atoms, others: [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: 494 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580627 none COC1=CC=C(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 35, 35, 9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 44, 44, 44, 44, 44, 1, 1, 35, 35, 35, 35, 35, 35, 35, 1, 1, 4, 10, 10, 10, 10, 1, 35, 35] 201 rigid atoms, others: [32, 38, 6, 7, 8, 9, 10, 11, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 194 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580627 none COC1=CC=C(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 35, 35, 35, 35, 43, 43, 43, 103, 103, 201, 201, 201, 201, 201, 35, 35, 1, 1, 2, 2, 2, 1, 1, 35, 35, 43, 103, 103, 103, 103, 35, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 24, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 506 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580627 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580627 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580627/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580627 Building REAL300025580628 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580628' /scratch/stefan/7787361/working/building/REAL300025580628 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580628 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580628/0 /scratch/stefan/7787361/working/building/REAL300025580628 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/123 `/scratch/stefan/7787361/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C1=CC=CN=C1) `REAL300025580628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580628 none CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 27, 27, 27, 75, 87, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 27, 75, 75, 87, 87, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 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]) total number of confs: 510 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580628 none CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 82, 82, 82, 24, 8, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 201, 201, 201, 201, 201, 116, 116, 116, 81, 24, 24, 8, 8, 116, 201, 201, 201, 201] 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, 34, 35]) total number of confs: 498 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580628 none CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 22, 32, 115, 115, 115, 116, 116, 1, 1, 1, 7, 7, 7, 7, 7, 2, 2, 2, 6, 21, 21, 32, 32, 1, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580628 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580628 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580628/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580628 Building REAL300025580629 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580629' /scratch/stefan/7787361/working/building/REAL300025580629 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580629 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580629/0 /scratch/stefan/7787361/working/building/REAL300025580629 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/124 `/scratch/stefan/7787361/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=C(Br)C=C2S1) `REAL300025580629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580629 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=C(Br)C=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 12, 65, 87, 143, 143, 143, 143, 143, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 64, 64, 87, 87, 1, 1, 1, 1] 143 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 444 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580629 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=C(Br)C=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [75, 75, 22, 8, 1, 1, 1, 1, 1, 1, 1, 74, 142, 142, 142, 142, 142, 142, 142, 142, 142, 74, 22, 22, 8, 8, 142, 142, 142, 142] 143 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580629 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580629 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580629/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580629 Building REAL300025580630 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580630' /scratch/stefan/7787361/working/building/REAL300025580630 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580630 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580630/0 /scratch/stefan/7787361/working/building/REAL300025580630 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/125 `/scratch/stefan/7787361/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)=C1) `REAL300025580630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580630 none COC1=CC=CC(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 145, 48, 48, 48, 48, 35, 35, 35, 11, 7, 1, 1, 1, 1, 1, 1, 1, 48, 48, 201, 201, 201, 201, 201, 201, 201, 48, 48, 35, 11, 11, 7, 7, 48, 201] 201 rigid atoms, others: [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]) total number of confs: 366 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580630 none COC1=CC=CC(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 3, 3, 4, 16, 22, 48, 48, 48, 48, 48, 1, 1, 19, 23, 23, 23, 19, 19, 19, 1, 1, 4, 16, 16, 22, 22, 1, 19] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580630 none COC1=CC=CC(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 19, 32, 32, 32, 91, 113, 201, 201, 201, 201, 201, 19, 19, 1, 3, 3, 3, 1, 1, 1, 19, 19, 32, 91, 91, 113, 113, 19, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 40, 25, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 616 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580630 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580630 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580630/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580630 Building REAL300025580631 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580631' /scratch/stefan/7787361/working/building/REAL300025580631 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580631 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580631/0 /scratch/stefan/7787361/working/building/REAL300025580631 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/126 `/scratch/stefan/7787361/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C2=CC=CC=C2N=C1C1=CC=CC=C1)NCCC1=NC(=O)O[N-]1) `REAL300025580631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580631 none O=C(CN1C2=CC=CC=C2N=C1C1=CC=CC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 15, 8, 1, 1, 1, 1, 1, 1, 1, 152, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 43, 15, 15, 8, 8] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 643 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580631 none O=C(CN1C2=CC=CC=C2N=C1C1=CC=CC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 49, 49, 126, 127, 201, 201, 201, 201, 201, 15, 15, 4, 4, 4, 4, 1, 1, 1, 1, 1, 49, 126, 126, 127, 127] 201 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, 41, 42]) total number of confs: 629 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580631 none O=C(CN1C2=CC=CC=C2N=C1C1=CC=CC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 25, 25, 97, 102, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 4, 4, 2, 4, 4, 25, 97, 97, 102, 102] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 563 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580631 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580631 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580631/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580631 Building REAL300025580632 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580632' /scratch/stefan/7787361/working/building/REAL300025580632 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580632 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580632/0 /scratch/stefan/7787361/working/building/REAL300025580632 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/127 `/scratch/stefan/7787361/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(OCC(=O)NCCC2=NC(=O)O[N-]2)C=C1Br) `REAL300025580632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580632 none N#CC1=CC=C(OCC(=O)NCCC2=NC(=O)O[N-]2)C=C1Br NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 199, 129, 76, 31, 31, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 84, 84, 30, 9, 9, 8, 8, 201] 201 rigid atoms, others: [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: 525 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580632 none N#CC1=CC=C(OCC(=O)NCCC2=NC(=O)O[N-]2)C=C1Br NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 18, 60, 60, 60, 121, 121, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 18, 18, 60, 121, 121, 121, 121, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 593 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580632 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580632 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580632/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580632 Building REAL300025580633 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580633' /scratch/stefan/7787361/working/building/REAL300025580633 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580633 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580633/0 /scratch/stefan/7787361/working/building/REAL300025580633 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/128 `/scratch/stefan/7787361/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Br)C=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580633 none CC1=CC=C(Br)C=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 126, 27, 27, 27, 13, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 126, 126, 27, 13, 13, 7, 7] 201 rigid atoms, others: [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: 591 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580633 none CC1=CC=C(Br)C=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 33, 33, 33, 102, 102, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 6, 6, 33, 102, 102, 102, 102] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 560 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580633 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580633 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580633/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580633 Building REAL300025580634 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580634' /scratch/stefan/7787361/working/building/REAL300025580634 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580634 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580634/0 /scratch/stefan/7787361/working/building/REAL300025580634 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/129 `/scratch/stefan/7787361/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C(N2C=CN=C2)=C1) `REAL300025580634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580634 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C(N2C=CN=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 11, 11, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 11, 59, 78, 201, 201, 201, 201, 201, 5, 4, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 11, 59, 59, 78, 78, 5, 5, 1, 1, 1, 5] 201 rigid atoms, others: [32, 33, 34, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 482 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580634 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C(N2C=CN=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 11, 11, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 39, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 5, 5, 1, 5, 29, 29, 39, 39, 1, 1, 5, 5, 5, 1] 201 rigid atoms, others: [1, 35, 11, 12, 13, 14, 15, 18, 19, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580634 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C(N2C=CN=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 11, 11, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 19, 8, 1, 1, 1, 1, 1, 1, 1, 38, 102, 102, 102, 102, 102, 102, 102, 102, 201, 201, 201, 201, 102, 38, 19, 19, 8, 8, 102, 102, 201, 201, 201, 102] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580634 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580634 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580634/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580634 Building REAL300025580635 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580635' /scratch/stefan/7787361/working/building/REAL300025580635 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580635 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580635/0 /scratch/stefan/7787361/working/building/REAL300025580635 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/130 `/scratch/stefan/7787361/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)O1) `REAL300025580635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580635 none CC1=NN=C(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 127, 69, 69, 69, 69, 37, 37, 37, 15, 7, 1, 1, 1, 1, 1, 1, 1, 69, 69, 201, 201, 201, 201, 127, 127, 37, 15, 15, 7, 7, 69, 69, 69] 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]) total number of confs: 637 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580635 none CC1=NN=C(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 28, 34, 69, 69, 69, 69, 69, 1, 1, 14, 14, 14, 14, 4, 4, 10, 28, 28, 34, 34, 2, 2, 2] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 21, 22] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580635 none CC1=NN=C(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 14, 52, 52, 52, 111, 122, 201, 201, 201, 201, 201, 14, 14, 1, 2, 2, 2, 6, 6, 52, 111, 111, 122, 122, 14, 14, 14] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580635 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580635 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580635/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580635 Building REAL300025580636 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580636' /scratch/stefan/7787361/working/building/REAL300025580636 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580636 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580636/0 /scratch/stefan/7787361/working/building/REAL300025580636 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/131 `/scratch/stefan/7787361/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CC=C2N=C1C1CC1) `REAL300025580636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580636 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CC=C2N=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 8, 31, 31, 91, 111, 201, 201, 201, 201, 201, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 31, 91, 91, 111, 111, 8, 8, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 569 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580636 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CC=C2N=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 46, 68, 162, 162, 162, 162, 162, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 10, 46, 46, 68, 68, 1, 1, 1, 1, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 439 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580636 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CC=C2N=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 24, 8, 1, 1, 1, 1, 1, 1, 1, 87, 162, 162, 162, 162, 162, 162, 162, 162, 162, 162, 201, 201, 86, 25, 25, 8, 8, 162, 162, 162, 162, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 550 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580636 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580636 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580636/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580636 Building REAL300025580637 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580637' /scratch/stefan/7787361/working/building/REAL300025580637 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580637 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580637/0 /scratch/stefan/7787361/working/building/REAL300025580637 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/132 `/scratch/stefan/7787361/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C(=O)C(F)(F)C2=CC([N+](=O)[O-])=CC=C21)NCCC1=NC(=O)O[N-]1) `REAL300025580637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580637 none O=C(CN1C(=O)C(F)(F)C2=CC([N+](=O)[O-])=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 15, 15, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 167, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 167, 167, 201, 201, 201, 54, 17, 17, 8, 8] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 690 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580637 none O=C(CN1C(=O)C(F)(F)C2=CC([N+](=O)[O-])=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 15, 15, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 113, 121, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 32, 113, 113, 121, 121] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 34, 35, 36, 33, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 594 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580637 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580637 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580637/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580637 Building REAL300025580638 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580638' /scratch/stefan/7787361/working/building/REAL300025580638 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580638 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580638/0 /scratch/stefan/7787361/working/building/REAL300025580638 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/133 `/scratch/stefan/7787361/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C1=CN(C)N=C1) `REAL300025580638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580638 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 1, 1, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 30, 30, 30, 101, 119, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 30, 101, 101, 119, 119, 1, 2, 2, 2, 1] 201 rigid atoms, others: [35, 16, 17, 18, 19, 20, 21, 22, 31] 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, 32, 33, 34]) total number of confs: 597 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580638 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 1, 1, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 79, 79, 79, 21, 8, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 201, 201, 201, 201, 201, 152, 152, 152, 79, 21, 21, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 466 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580638 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 1, 1, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 10, 48, 62, 152, 152, 152, 152, 152, 1, 1, 1, 1, 7, 7, 7, 7, 7, 2, 2, 2, 10, 48, 48, 62, 62, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17] set([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, 34, 35]) total number of confs: 390 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580638 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580638 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580638/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580638 Building REAL300025580639 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580639' /scratch/stefan/7787361/working/building/REAL300025580639 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580639 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580639/0 /scratch/stefan/7787361/working/building/REAL300025580639 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/134 `/scratch/stefan/7787361/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC=C1Cl) `REAL300025580639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580639 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 33, 33, 117, 121, 201, 201, 201, 201, 201, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 33, 117, 117, 121, 121, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 563 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580639 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 66, 71, 158, 158, 158, 158, 158, 1, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 6, 13, 66, 66, 71, 71, 1, 1, 6, 6, 2, 6] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 392 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580639 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 57, 158, 158, 158, 158, 158, 201, 201, 197, 201, 201, 201, 57, 19, 19, 8, 8, 158, 158, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 568 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580639 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580639 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580639/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580639 Building REAL300025580640 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580640' /scratch/stefan/7787361/working/building/REAL300025580640 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580640 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580640/0 /scratch/stefan/7787361/working/building/REAL300025580640 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/135 `/scratch/stefan/7787361/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(Br)=C1) `REAL300025580640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580640 none CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 154, 201, 168, 114, 29, 29, 29, 13, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 114, 114, 29, 13, 13, 8, 8, 201] 201 rigid atoms, others: [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]) total number of confs: 842 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580640 none CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 34, 34, 34, 116, 116, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 34, 116, 116, 116, 116, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 17, 18, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 593 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580640 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580640 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580640/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580640 Building REAL300025580641 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580641' /scratch/stefan/7787361/working/building/REAL300025580641 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580641 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580641/0 /scratch/stefan/7787361/working/building/REAL300025580641 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/136 `/scratch/stefan/7787361/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC2=CC=CC=C2C(=O)N1)NCCC1=NC(=O)O[N-]1) `REAL300025580641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580641 none O=C(CC1=CC2=CC=CC=C2C(=O)N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 106, 106, 201, 201, 201, 201, 201, 201, 37, 17, 17, 8, 8] 201 rigid atoms, others: [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: 567 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580641 none O=C(CC1=CC2=CC=CC=C2C(=O)N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 113, 115, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 31, 113, 113, 115, 115] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30] set([0, 1, 34, 35, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580641 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580641 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580641/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580641 Building REAL300025580642 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580642' /scratch/stefan/7787361/working/building/REAL300025580642 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580642 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580642/0 /scratch/stefan/7787361/working/building/REAL300025580642 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/137 `/scratch/stefan/7787361/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1COC2=CC=CC=C2O1)NCCC1=NC(=O)O[N-]1) `REAL300025580642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580642 none O=C(CC1COC2=CC=CC=C2O1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 146, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 146, 146, 201, 201, 201, 201, 201, 201, 201, 56, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 745 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580642 none O=C(CC1COC2=CC=CC=C2O1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 111, 116, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 33, 111, 111, 116, 116] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 34, 35, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/7787361/working/building/REAL300025580642 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580642 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580642/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580642 Building REAL300025580643 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580643' /scratch/stefan/7787361/working/building/REAL300025580643 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580643 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580643/0 /scratch/stefan/7787361/working/building/REAL300025580643 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/138 `/scratch/stefan/7787361/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(OC(F)F)=C1) `REAL300025580643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580643 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(OC(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 12, 5, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 35, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 5, 20, 20, 1, 5, 29, 29, 35, 35, 1, 1, 19, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 20, 26, 27, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 21, 22, 23, 24, 25, 28]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580643 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(OC(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 12, 5, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 17, 8, 1, 1, 1, 1, 1, 1, 1, 58, 147, 147, 147, 147, 147, 182, 201, 201, 147, 58, 17, 17, 8, 8, 147, 147, 201, 147] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 505 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580643 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580643 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580643/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580643 Building REAL300025580644 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580644' /scratch/stefan/7787361/working/building/REAL300025580644 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580644 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580644/0 /scratch/stefan/7787361/working/building/REAL300025580644 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/139 `/scratch/stefan/7787361/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1OC) `REAL300025580644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580644 none COC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 125, 125, 125, 125, 93, 31, 31, 31, 15, 7, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 201, 201, 201, 201, 125, 125, 93, 93, 31, 15, 15, 7, 7, 201, 201, 201] 201 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, 37]) total number of confs: 721 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580644 none COC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 25, 25, 25, 63, 63, 125, 125, 125, 125, 125, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 5, 5, 25, 63, 63, 63, 63, 5, 5, 5] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580644 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580644 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580644/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580644 Building REAL300025580645 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580645' /scratch/stefan/7787361/working/building/REAL300025580645 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580645 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580645/0 /scratch/stefan/7787361/working/building/REAL300025580645 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/140 `/scratch/stefan/7787361/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1) `REAL300025580645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580645 none CC(C)(C)OC(=O)NC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 198, 151, 198, 151, 57, 57, 57, 18, 8, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 57, 19, 19, 8, 8, 151, 151, 151, 151, 151, 151] 201 rigid atoms, others: [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, 40, 41, 42, 43]) total number of confs: 644 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580645 none CC(C)(C)OC(=O)NC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 5, 3, 5, 1, 1, 1, 11, 11, 11, 55, 71, 151, 151, 151, 151, 151, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 11, 55, 55, 71, 71, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 38, 7, 8, 9, 42, 39, 40, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 427 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580645 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580645 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580645/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580645 Building REAL300025580646 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580646' /scratch/stefan/7787361/working/building/REAL300025580646 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580646 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580646/0 /scratch/stefan/7787361/working/building/REAL300025580646 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/141 `/scratch/stefan/7787361/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC(Cl)=C2)CC1) `REAL300025580646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580646 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC(Cl)=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 13, 23, 23, 94, 101, 201, 201, 201, 201, 201, 3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 23, 94, 94, 101, 101, 3, 3, 1, 1, 1, 1, 13, 13, 13, 13] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 562 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580646 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC(Cl)=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 23, 89, 89, 89, 89, 89, 1, 1, 7, 13, 13, 13, 13, 13, 13, 1, 1, 4, 16, 16, 23, 23, 7, 7, 13, 13, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 33, 11, 12, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580646 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC(Cl)=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 8, 1, 1, 1, 1, 1, 1, 1, 53, 89, 165, 201, 201, 201, 201, 201, 201, 89, 89, 53, 20, 20, 8, 8, 165, 165, 201, 201, 201, 201, 89, 89, 89, 89] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580646 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580646 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580646/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580646 Building REAL300025580647 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580647' /scratch/stefan/7787361/working/building/REAL300025580647 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580647 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580647/0 /scratch/stefan/7787361/working/building/REAL300025580647 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/142 `/scratch/stefan/7787361/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C([N+](=O)[O-])C=C1F) `REAL300025580647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580647 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 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: [192, 192, 192, 192, 113, 113, 113, 24, 8, 1, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 113, 24, 24, 8, 8, 192] 192 rigid atoms, others: [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]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580647 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 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: [4, 1, 1, 1, 1, 1, 7, 7, 7, 37, 59, 192, 192, 192, 192, 192, 1, 1, 2, 2, 1, 1, 1, 4, 4, 4, 1, 7, 37, 37, 59, 59, 1] 192 rigid atoms, others: [32, 1, 2, 3, 4, 5, 16, 17, 20, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 430 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580647 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580647 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580647/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580647 Building REAL300025580648 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580648' /scratch/stefan/7787361/working/building/REAL300025580648 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580648 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580648/0 /scratch/stefan/7787361/working/building/REAL300025580648 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/143 `/scratch/stefan/7787361/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC1C1=CC=CC=C1Cl) `REAL300025580648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580648 none O=C(NCCC1=NC(=O)O[N-]1)C1CC1C1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 14, 14, 60, 83, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 14, 60, 60, 83, 83, 4, 4, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 503 number of broken/clashed sets: 27 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580648 none O=C(NCCC1=NC(=O)O[N-]1)C1CC1C1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 40, 62, 175, 175, 175, 175, 175, 1, 1, 1, 1, 4, 4, 2, 4, 4, 4, 9, 40, 40, 62, 62, 1, 1, 1, 1, 4, 4, 2, 4] 201 rigid atoms, others: [1, 11, 12, 13, 14, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 411 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580648 none O=C(NCCC1=NC(=O)O[N-]1)C1CC1C1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 82, 175, 175, 175, 201, 201, 201, 201, 201, 201, 81, 24, 24, 8, 8, 175, 175, 175, 175, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 590 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580648 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580648 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580648/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580648 Building REAL300025580649 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580649' /scratch/stefan/7787361/working/building/REAL300025580649 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580649 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580649/0 /scratch/stefan/7787361/working/building/REAL300025580649 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/144 `/scratch/stefan/7787361/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(C(=O)NCCC2=NC(=O)O[N-]2)C2(CC2)C1) `REAL300025580649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580649 none CC(C)(C)OC(=O)N1CC(C(=O)NCCC2=NC(=O)O[N-]2)C2(CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 179, 120, 179, 120, 120, 40, 40, 40, 19, 8, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 120, 40, 19, 19, 8, 8, 120, 120, 120, 120, 120, 120] 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 642 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580649 none CC(C)(C)OC(=O)N1CC(C(=O)NCCC2=NC(=O)O[N-]2)C2(CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 10, 9, 2, 1, 2, 1, 1, 1, 1, 8, 8, 8, 43, 49, 120, 120, 120, 120, 120, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 8, 43, 43, 49, 49, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 43, 44, 45, 46, 47, 21, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 316 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580649 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580649 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580649/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580649 Building REAL300025580650 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580650' /scratch/stefan/7787361/working/building/REAL300025580650 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580650 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580650/0 /scratch/stefan/7787361/working/building/REAL300025580650 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/145 `/scratch/stefan/7787361/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CSC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580650 none CC(C)(C)OC(=O)N1CSC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 164, 121, 164, 121, 121, 121, 121, 68, 121, 68, 68, 23, 9, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 121, 121, 121, 121, 68, 23, 23, 9, 9] 201 rigid atoms, others: [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]) total number of confs: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580650 none CC(C)(C)OC(=O)N1CSC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 11, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 34, 43, 121, 121, 121, 121, 121, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 34, 34, 43, 43] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580650 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580650 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580650/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580650 Building REAL300025580651 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580651' /scratch/stefan/7787361/working/building/REAL300025580651 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580651 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580651/0 /scratch/stefan/7787361/working/building/REAL300025580651 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/146 `/scratch/stefan/7787361/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC=CC=C1Br) `REAL300025580651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580651 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 1, 1, 1, 1, 1, 1, 17, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 6, 29, 29, 99, 107, 201, 201, 201, 201, 201, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 29, 99, 99, 107, 107, 1, 1, 1, 1] 201 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25]) total number of confs: 565 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580651 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 1, 1, 1, 1, 1, 1, 17, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 1, 1, 1, 1, 1, 1, 1, 51, 160, 160, 160, 193, 201, 201, 201, 201, 201, 51, 17, 17, 7, 7, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 707 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580651 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580651 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580651/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580651 Building REAL300025580652 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580652' /scratch/stefan/7787361/working/building/REAL300025580652 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580652 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580652/0 /scratch/stefan/7787361/working/building/REAL300025580652 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/147 `/scratch/stefan/7787361/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(S(=O)(=O)C2CC2)C=C1) `REAL300025580652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580652 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(S(=O)(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 17, 31, 31, 108, 125, 201, 201, 201, 201, 201, 17, 17, 17, 9, 1, 9, 9, 1, 1, 1, 17, 17, 31, 108, 108, 125, 125, 17, 17, 1, 1, 1, 1, 1, 17, 17] 201 rigid atoms, others: [32, 33, 34, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 636 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580652 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(S(=O)(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 21, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 2, 2, 2, 17, 17, 1, 1, 3, 15, 15, 21, 21, 1, 1, 17, 17, 17, 17, 17, 1, 1] 201 rigid atoms, others: [1, 35, 36, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 198 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580652 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(S(=O)(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 19, 8, 1, 1, 1, 1, 1, 1, 1, 52, 80, 80, 52, 52, 125, 125, 125, 201, 201, 80, 80, 52, 19, 19, 8, 8, 80, 80, 201, 201, 201, 201, 201, 80, 80] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 925 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580652 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580652 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580652/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580652 Building REAL300025580653 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580653' /scratch/stefan/7787361/working/building/REAL300025580653 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580653 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580653/0 /scratch/stefan/7787361/working/building/REAL300025580653 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/148 `/scratch/stefan/7787361/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@H]1CCCN1S(=O)(=O)C1=CC=CC=C1) `REAL300025580653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580653 none O=C(NCCC1=NC(=O)O[N-]1)[C@H]1CCCN1S(=O)(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 14, 29, 29, 91, 104, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 29, 91, 91, 104, 104, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 17, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 576 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580653 none O=C(NCCC1=NC(=O)O[N-]1)[C@H]1CCCN1S(=O)(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 23, 36, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 6, 14, 14, 6, 23, 23, 36, 36, 1, 1, 1, 1, 1, 1, 14, 14, 6, 14, 14] 201 rigid atoms, others: [32, 1, 34, 35, 36, 33, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41]) total number of confs: 305 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580653 none O=C(NCCC1=NC(=O)O[N-]1)[C@H]1CCCN1S(=O)(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 9, 1, 1, 1, 1, 1, 1, 1, 72, 111, 111, 111, 111, 111, 111, 201, 201, 201, 201, 201, 201, 201, 201, 72, 25, 25, 9, 9, 111, 111, 111, 111, 111, 111, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 784 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580653 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580653 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580653/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580653 Building REAL300025580654 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580654' /scratch/stefan/7787361/working/building/REAL300025580654 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580654 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580654/0 /scratch/stefan/7787361/working/building/REAL300025580654 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/149 `/scratch/stefan/7787361/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)SC=C1) `REAL300025580654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580654 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)SC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 38, 66, 170, 170, 170, 170, 170, 1, 1, 1, 1, 1, 1, 7, 38, 38, 66, 66, 1, 1] 170 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) total number of confs: 444 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580654 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)SC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 99, 170, 170, 170, 170, 170, 99, 25, 25, 8, 8, 170, 170] 170 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580654 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580654 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580654/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580654 Building REAL300025580655 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580655' /scratch/stefan/7787361/working/building/REAL300025580655 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580655 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580655/0 /scratch/stefan/7787361/working/building/REAL300025580655 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/150 `/scratch/stefan/7787361/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC(F)(F)F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580655 none COC1=CC=C(OC(F)(F)F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 113, 113, 113, 113, 113, 113, 179, 201, 201, 201, 63, 63, 63, 17, 8, 1, 1, 1, 1, 1, 1, 1, 113, 133, 133, 133, 113, 113, 63, 17, 17, 8, 8, 113] 201 rigid atoms, others: [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]) total number of confs: 564 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580655 none COC1=CC=C(OC(F)(F)F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 1, 1, 5, 5, 5, 23, 29, 113, 113, 113, 113, 113, 1, 2, 2, 2, 1, 1, 5, 23, 23, 29, 29, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 34, 23, 27, 28] set([0, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580655 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580655 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580655/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580655 Building REAL300025580656 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580656' /scratch/stefan/7787361/working/building/REAL300025580656 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580656 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580656/0 /scratch/stefan/7787361/working/building/REAL300025580656 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/151 `/scratch/stefan/7787361/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC2=C1OC(F)(F)O2) `REAL300025580656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580656 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC2=C1OC(F)(F)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 15, 15, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 86, 86, 86, 23, 8, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 86, 23, 23, 8, 8, 138, 138] 138 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580656 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC2=C1OC(F)(F)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 15, 15, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [1, 1, 1, 1, 9, 9, 9, 52, 78, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 52, 52, 78, 78, 1, 1] 138 rigid atoms, others: [0, 1, 2, 3, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580656 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580656 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580656/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580656 Building REAL300025580657 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580657' /scratch/stefan/7787361/working/building/REAL300025580657 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580657 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580657/0 /scratch/stefan/7787361/working/building/REAL300025580657 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/152 `/scratch/stefan/7787361/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl) `REAL300025580657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580657 none COC1=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 175, 175, 175, 112, 41, 41, 41, 15, 7, 1, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 201, 201, 201, 175, 112, 112, 41, 15, 15, 7, 7, 175, 175] 201 rigid atoms, others: [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]) total number of confs: 628 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580657 none COC1=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 13, 13, 13, 61, 67, 175, 175, 175, 175, 175, 1, 1, 1, 1, 3, 3, 3, 1, 4, 4, 13, 61, 61, 67, 67, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 17, 18, 19, 20, 24] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580657 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580657 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580657/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580657 Building REAL300025580658 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580658' /scratch/stefan/7787361/working/building/REAL300025580658 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580658 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580658/0 /scratch/stefan/7787361/working/building/REAL300025580658 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/153 `/scratch/stefan/7787361/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)N[C@@H](CC(C)C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580658 none CC1=CC=C(S(=O)(=O)N[C@@H](CC(C)C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 197, 197, 119, 197, 197, 72, 31, 72, 72, 76, 76, 76, 31, 31, 16, 8, 1, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 197, 197, 119, 76, 76, 76, 76, 76, 76, 76, 76, 76, 31, 16, 16, 8, 8, 197, 197] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 870 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580658 none CC1=CC=C(S(=O)(=O)N[C@@H](CC(C)C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 14, 14, 18, 18, 18, 14, 33, 33, 33, 101, 105, 197, 197, 197, 197, 197, 1, 1, 2, 2, 2, 1, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 33, 101, 101, 105, 105, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 48, 49, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 614 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580658 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580658 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580658/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580658 Building REAL300025580659 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580659' /scratch/stefan/7787361/working/building/REAL300025580659 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580659 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580659/0 /scratch/stefan/7787361/working/building/REAL300025580659 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/154 `/scratch/stefan/7787361/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CSCC1=CC=C(Br)C=C1)NCCC1=NC(=O)O[N-]1) `REAL300025580659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580659 none O=C(CSCC1=CC=C(Br)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 14, 5, 1, 1, 1, 1, 17, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 129, 158, 201, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 129, 129, 201, 201, 201, 201, 201, 201, 40, 8, 8, 8, 8] 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]) total number of confs: 734 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580659 none O=C(CSCC1=CC=C(Br)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 14, 5, 1, 1, 1, 1, 17, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 33, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 131, 131, 201, 201, 201, 201, 201, 33, 33, 3, 3, 1, 1, 1, 1, 73, 131, 131, 131, 131] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 645 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580659 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580659 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580659/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580659 Building REAL300025580660 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580660' /scratch/stefan/7787361/working/building/REAL300025580660 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580660 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580660/0 /scratch/stefan/7787361/working/building/REAL300025580660 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/155 `/scratch/stefan/7787361/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=C(O)C2=CC=CC=C2C=C1)NCCC1=NC(=O)O[N-]1) `REAL300025580660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580660 none O=C(CCC1=C(O)C2=CC=CC=C2C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 162, 180, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 162, 162, 180, 180, 402, 201, 201, 201, 201, 201, 201, 57, 19, 19, 8, 8] 402 rigid atoms, others: [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]) total number of confs: 1162 number of broken/clashed sets: 402 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580660 none O=C(CCC1=C(O)C2=CC=CC=C2C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [28, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 103, 109, 201, 201, 201, 201, 201, 8, 8, 5, 5, 2, 1, 1, 1, 1, 1, 1, 28, 104, 104, 109, 109] 402 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39]) total number of confs: 580 number of broken/clashed sets: 402 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580660 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580660 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580660/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580660 Building REAL300025580661 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580661' /scratch/stefan/7787361/working/building/REAL300025580661 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580661 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580661/0 /scratch/stefan/7787361/working/building/REAL300025580661 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/156 `/scratch/stefan/7787361/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(F)(F)F)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580661 none CN1N=C(C(F)(F)F)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 139, 139, 139, 139, 139, 81, 81, 81, 23, 8, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 81, 23, 23, 8, 8] 139 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]) total number of confs: 352 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580661 none CN1N=C(C(F)(F)F)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 13, 13, 13, 62, 82, 139, 139, 139, 139, 139, 2, 2, 2, 1, 13, 62, 62, 82, 82] 139 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 24] set([5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 439 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580661 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580661 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580661/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580661 Building REAL300025580662 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580662' /scratch/stefan/7787361/working/building/REAL300025580662 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580662 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580662/0 /scratch/stefan/7787361/working/building/REAL300025580662 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/157 `/scratch/stefan/7787361/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=C1N=C(NC1=CC=CC=C1)S2) `REAL300025580662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580662 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=C1N=C(NC1=CC=CC=C1)S2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 43, 43, 111, 115, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 14, 43, 111, 111, 115, 115, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 583 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580662 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=C1N=C(NC1=CC=CC=C1)S2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 28, 32, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 10, 14, 14, 1, 8, 28, 28, 32, 32, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 10, 14, 14] 201 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580662 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=C1N=C(NC1=CC=CC=C1)S2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 1, 1, 1, 1, 1, 1, 1, 68, 102, 102, 102, 102, 102, 102, 102, 102, 191, 201, 201, 201, 201, 201, 102, 68, 21, 21, 7, 7, 102, 102, 102, 102, 102, 102, 102, 191, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 629 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580662 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580662 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580662/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580662 Building REAL300025580663 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580663' /scratch/stefan/7787361/working/building/REAL300025580663 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580663 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580663/0 /scratch/stefan/7787361/working/building/REAL300025580663 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/158 `/scratch/stefan/7787361/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025580663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580663 none CC(C)(C)C(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 166, 166, 166, 166, 80, 80, 80, 24, 8, 1, 1, 1, 1, 1, 1, 1, 166, 166, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 166, 166, 79, 24, 25, 8, 8, 166] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 526 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580663 none CC(C)(C)C(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 55, 166, 166, 166, 166, 166, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 1, 1, 5, 29, 29, 55, 55, 1] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 12, 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: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580663 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580663 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580663/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580663 Building REAL300025580664 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580664' /scratch/stefan/7787361/working/building/REAL300025580664 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580664 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580664/0 /scratch/stefan/7787361/working/building/REAL300025580664 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/159 `/scratch/stefan/7787361/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Br) `REAL300025580664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580664 none CC1=CC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 149, 149, 97, 97, 97, 20, 8, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 149, 149, 149, 149, 149, 149, 96, 20, 20, 8, 8, 149] 149 rigid atoms, others: [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]) total number of confs: 373 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580664 none CC1=CC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 47, 70, 149, 149, 149, 149, 149, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 47, 47, 70, 70, 1] 149 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 17, 18, 19, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580664 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580664 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580664/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580664 Building REAL300025580665 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580665' /scratch/stefan/7787361/working/building/REAL300025580665 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580665 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580665/0 /scratch/stefan/7787361/working/building/REAL300025580665 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/160 `/scratch/stefan/7787361/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1Cl) `REAL300025580665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580665 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 147, 91, 91, 91, 20, 8, 1, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 147, 147, 147, 147, 147, 91, 20, 20, 8, 8] 147 rigid atoms, others: [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]) total number of confs: 361 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580665 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 63, 147, 147, 147, 147, 147, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 39, 39, 63, 63] 147 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580665 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580665 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580665/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580665 Building REAL300025580666 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580666' /scratch/stefan/7787361/working/building/REAL300025580666 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580666 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580666/0 /scratch/stefan/7787361/working/building/REAL300025580666 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/161 `/scratch/stefan/7787361/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)N(C(=O)OC(C)(C)C)C1) `REAL300025580666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580666 none COC(=O)C[C@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)N(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 114, 167, 63, 63, 63, 63, 31, 63, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 63, 63, 83, 83, 96, 96, 96, 96, 63, 167, 167, 167, 114, 114, 63, 63, 31, 9, 9, 9, 9, 96, 96, 96, 96, 96, 96, 96, 96, 96, 63, 63] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 730 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580666 none COC(=O)C[C@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)N(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 5, 22, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 63, 63, 63, 63, 63, 1, 1, 2, 2, 5, 5, 5, 5, 1, 22, 22, 22, 5, 5, 1, 1, 5, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 51, 52, 21, 22, 36, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580666 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580666 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580666/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580666 Building REAL300025580667 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580667' /scratch/stefan/7787361/working/building/REAL300025580667 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580667 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580667/0 /scratch/stefan/7787361/working/building/REAL300025580667 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/162 `/scratch/stefan/7787361/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(NC2=CC(F)=CC(F)=C2)=N1) `REAL300025580667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580667 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(NC2=CC(F)=CC(F)=C2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 8, 1, 1, 1, 15, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 17, 32, 32, 98, 118, 201, 201, 201, 201, 201, 17, 17, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 32, 98, 98, 118, 118, 17, 8, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 589 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580667 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(NC2=CC(F)=CC(F)=C2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 8, 1, 1, 1, 15, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 17, 23, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 7, 15, 15, 15, 10, 15, 15, 15, 1, 4, 17, 17, 23, 23, 1, 7, 15, 10, 15] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 24, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580667 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(NC2=CC(F)=CC(F)=C2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 8, 1, 1, 1, 15, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 67, 81, 81, 81, 81, 177, 201, 201, 201, 195, 201, 201, 201, 81, 67, 25, 25, 8, 8, 81, 177, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 629 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580667 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580667 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580667/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580667 Building REAL300025580668 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580668' /scratch/stefan/7787361/working/building/REAL300025580668 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580668 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580668/0 /scratch/stefan/7787361/working/building/REAL300025580668 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/163 `/scratch/stefan/7787361/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)OC(C)(C)C)C(CC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580668 none CN(C(=O)OC(C)(C)C)C(CC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 75, 125, 174, 174, 201, 201, 201, 201, 75, 75, 75, 75, 75, 75, 75, 75, 24, 8, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 25, 25, 8, 8] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 664 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580668 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580668 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580668/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580668 Building REAL300025580669 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580669' /scratch/stefan/7787361/working/building/REAL300025580669 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580669 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580669/0 /scratch/stefan/7787361/working/building/REAL300025580669 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/164 `/scratch/stefan/7787361/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NCCC2=NC(=O)O[N-]2)(C2=CC=CC(Cl)=C2)C1) `REAL300025580669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580669 none CC1CC(C(=O)NCCC2=NC(=O)O[N-]2)(C2=CC=CC(Cl)=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 19, 19, 19, 78, 102, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 19, 78, 78, 102, 102, 1, 1, 1, 1, 7, 7] 201 rigid atoms, others: [19, 34, 3, 36, 37, 15, 16, 17, 18, 35, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 575 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580669 none CC1CC(C(=O)NCCC2=NC(=O)O[N-]2)(C2=CC=CC(Cl)=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 76, 76, 76, 21, 8, 1, 1, 1, 1, 1, 1, 1, 128, 201, 201, 201, 201, 201, 201, 128, 128, 128, 128, 128, 128, 128, 76, 21, 21, 8, 8, 201, 201, 201, 201, 128, 128] 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, 34, 35, 36, 37, 38, 39]) total number of confs: 551 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580669 none CC1CC(C(=O)NCCC2=NC(=O)O[N-]2)(C2=CC=CC(Cl)=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 26, 39, 128, 128, 128, 128, 128, 1, 7, 7, 4, 7, 7, 7, 1, 2, 2, 2, 1, 1, 1, 5, 26, 26, 39, 39, 7, 7, 6, 7, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 38, 39, 15, 22, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 302 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580669 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580669 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580669/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580669 Building REAL300025580670 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580670' /scratch/stefan/7787361/working/building/REAL300025580670 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580670 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580670/0 /scratch/stefan/7787361/working/building/REAL300025580670 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/165 `/scratch/stefan/7787361/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC2=CC=CC=C21) `REAL300025580670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580670 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 132, 132, 93, 93, 93, 23, 8, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 132, 132, 132, 201, 201, 201, 201, 201, 93, 24, 24, 8, 8, 132, 132, 132, 132] 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, 34, 35]) total number of confs: 770 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580670 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 9, 9, 9, 41, 59, 132, 132, 132, 132, 132, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 41, 41, 59, 59, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 35, 33, 34, 15, 16, 17, 18, 19, 20, 21] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 370 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580670 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580670 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580670/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580670 Building REAL300025580671 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580671' /scratch/stefan/7787361/working/building/REAL300025580671 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580671 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580671/0 /scratch/stefan/7787361/working/building/REAL300025580671 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/166 `/scratch/stefan/7787361/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=C(N2CC(C(=O)NCCC3=NC(=O)O[N-]3)CC2=O)C=N1) `REAL300025580671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580671 none COCCN1C=C(N2CC(C(=O)NCCC3=NC(=O)O[N-]3)CC2=O)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 187, 107, 107, 107, 93, 93, 93, 34, 34, 34, 15, 8, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 107, 107, 201, 201, 201, 201, 201, 187, 187, 107, 93, 93, 93, 34, 15, 15, 8, 8, 93, 93, 107] 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, 41, 42, 43, 44]) total number of confs: 822 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580671 none COCCN1C=C(N2CC(C(=O)NCCC3=NC(=O)O[N-]3)CC2=O)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 11, 9, 2, 2, 2, 1, 1, 1, 1, 1, 9, 9, 9, 40, 41, 93, 93, 93, 93, 93, 1, 1, 1, 2, 2, 14, 14, 14, 11, 11, 9, 9, 3, 1, 1, 1, 9, 40, 40, 41, 41, 1, 1, 3] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 43, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 44]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580671 none COCCN1C=C(N2CC(C(=O)NCCC3=NC(=O)O[N-]3)CC2=O)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 8, 6, 1, 1, 1, 1, 1, 2, 2, 2, 14, 14, 14, 49, 50, 107, 107, 107, 107, 107, 2, 2, 3, 1, 1, 11, 11, 11, 8, 8, 6, 6, 1, 2, 2, 2, 14, 49, 49, 50, 50, 2, 2, 1] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 44, 24, 25] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580671 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580671 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580671/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580671 Building REAL300025580672 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580672' /scratch/stefan/7787361/working/building/REAL300025580672 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580672 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580672/0 /scratch/stefan/7787361/working/building/REAL300025580672 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/167 `/scratch/stefan/7787361/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580672 none C=CCOC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 176, 120, 83, 120, 120, 83, 36, 36, 36, 14, 8, 1, 1, 1, 1, 1, 1, 1, 120, 120, 201, 201, 201, 201, 201, 120, 120, 83, 83, 36, 14, 14, 8, 8, 120, 120] 201 rigid atoms, others: [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: 857 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580672 none C=CCOC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 3, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 42, 44, 120, 120, 120, 120, 120, 1, 1, 17, 17, 17, 5, 5, 1, 1, 5, 5, 11, 42, 42, 44, 44, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 36, 27, 28, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580672 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580672 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580672/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580672 Building REAL300025580673 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580673' /scratch/stefan/7787361/working/building/REAL300025580673 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580673 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580673/0 /scratch/stefan/7787361/working/building/REAL300025580673 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/168 `/scratch/stefan/7787361/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=NC(OC(F)F)=C1) `REAL300025580673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580673 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=NC(OC(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 8, 1, 12, 5, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 33, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 1, 5, 29, 29, 33, 33, 1, 17, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 21, 27, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 28]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580673 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=NC(OC(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 8, 1, 12, 5, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 54, 142, 142, 142, 142, 142, 142, 170, 201, 201, 142, 54, 17, 17, 8, 8, 142, 201, 142] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 549 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580673 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580673 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580673/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580673 Building REAL300025580674 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580674' /scratch/stefan/7787361/working/building/REAL300025580674 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580674 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580674/0 /scratch/stefan/7787361/working/building/REAL300025580674 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/169 `/scratch/stefan/7787361/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OCCC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580674 none CC(OCCC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 98, 129, 174, 201, 201, 201, 201, 201, 201, 47, 47, 19, 8, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 174, 174, 201, 201, 201, 201, 201, 201, 201, 47, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 822 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580674 none CC(OCCC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 20, 54, 54, 54, 114, 117, 201, 201, 201, 201, 201, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 1, 1, 1, 54, 114, 114, 117, 117] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39]) total number of confs: 612 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580674 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580674 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580674/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580674 Building REAL300025580675 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580675' /scratch/stefan/7787361/working/building/REAL300025580675 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580675 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580675/0 /scratch/stefan/7787361/working/building/REAL300025580675 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/170 `/scratch/stefan/7787361/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(N2CC(C(=O)NCCC3=NC(=O)O[N-]3)CC2=O)C=C1Cl) `REAL300025580675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580675 none N#CC1=CC=C(N2CC(C(=O)NCCC3=NC(=O)O[N-]3)CC2=O)C=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 81, 81, 81, 34, 34, 34, 16, 8, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 201, 201, 201, 201, 201, 81, 81, 81, 34, 16, 16, 8, 8, 81, 81, 201] 201 rigid atoms, others: [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: 430 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580675 none N#CC1=CC=C(N2CC(C(=O)NCCC3=NC(=O)O[N-]3)CC2=O)C=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 4, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 37, 38, 81, 81, 81, 81, 81, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 1, 9, 37, 37, 38, 38, 1, 1, 6] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 20, 21, 22, 28, 29, 30, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 38]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580675 none N#CC1=CC=C(N2CC(C(=O)NCCC3=NC(=O)O[N-]3)CC2=O)C=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 35, 35, 35, 109, 110, 201, 201, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 35, 109, 109, 110, 110, 6, 6, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 572 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580675 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580675 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580675/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580675 Building REAL300025580676 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580676' /scratch/stefan/7787361/working/building/REAL300025580676 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580676 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580676/0 /scratch/stefan/7787361/working/building/REAL300025580676 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/171 `/scratch/stefan/7787361/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1S(C)(=O)=O) `REAL300025580676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580676 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 119, 119, 167, 167, 75, 75, 75, 19, 8, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 201, 201, 201, 167, 167, 167, 167, 167, 75, 19, 19, 8, 8, 167, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 820 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580676 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 47, 167, 167, 167, 167, 167, 1, 1, 1, 7, 7, 7, 3, 3, 3, 1, 1, 5, 29, 29, 47, 47, 1, 7, 7, 7] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 17, 18, 19, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 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 /scratch/stefan/7787361/working/building/REAL300025580676 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580676 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580676/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580676 Building REAL300025580677 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580677' /scratch/stefan/7787361/working/building/REAL300025580677 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580677 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580677/0 /scratch/stefan/7787361/working/building/REAL300025580677 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/172 `/scratch/stefan/7787361/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2OC(F)(F)OC2=C1) `REAL300025580677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580677 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2OC(F)(F)OC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 42, 64, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 42, 42, 64, 64, 1, 1, 1] 120 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 356 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580677 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2OC(F)(F)OC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 23, 8, 1, 1, 1, 1, 1, 1, 1, 62, 120, 120, 120, 120, 120, 120, 120, 120, 120, 120, 61, 23, 23, 8, 8, 120, 120, 120] 120 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580677 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580677 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580677/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580677 Building REAL300025580678 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580678' /scratch/stefan/7787361/working/building/REAL300025580678 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580678 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580678/0 /scratch/stefan/7787361/working/building/REAL300025580678 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/173 `/scratch/stefan/7787361/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(OC)=C1) `REAL300025580678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580678 none CCCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 165, 165, 62, 34, 62, 62, 31, 31, 31, 15, 7, 1, 1, 1, 1, 1, 1, 1, 62, 62, 76, 62, 201, 201, 201, 201, 201, 165, 165, 62, 62, 31, 15, 15, 7, 7, 76, 76, 76, 62] 201 rigid atoms, others: [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, 39, 40]) total number of confs: 674 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580678 none CCCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 21, 62, 62, 62, 62, 62, 1, 1, 3, 1, 13, 13, 13, 13, 13, 5, 5, 1, 1, 4, 16, 16, 21, 21, 3, 3, 3, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 40, 19, 20, 22, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580678 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580678 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580678/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580678 Building REAL300025580679 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580679' /scratch/stefan/7787361/working/building/REAL300025580679 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580679 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580679/0 /scratch/stefan/7787361/working/building/REAL300025580679 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/174 `/scratch/stefan/7787361/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(CNC(=O)C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=C1) `REAL300025580679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580679 none CC1=CC=CC(CNC(=O)C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 195, 201, 201, 116, 65, 65, 26, 65, 26, 47, 47, 26, 26, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 47, 47, 201, 201, 201, 201, 195, 201, 201, 108, 108, 65, 47, 47, 26, 8, 8, 8, 8, 47, 47, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 626 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580679 none CC1=CC=CC(CNC(=O)C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 21, 30, 30, 12, 3, 3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 47, 47, 47, 47, 47, 1, 1, 30, 30, 30, 30, 21, 30, 30, 12, 12, 3, 1, 1, 5, 19, 19, 19, 19, 1, 1, 30] 201 rigid atoms, others: [37, 38, 8, 44, 10, 11, 12, 13, 14, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 46]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580679 none CC1=CC=CC(CNC(=O)C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 30, 30, 19, 30, 77, 77, 77, 103, 103, 201, 201, 201, 201, 201, 30, 30, 1, 2, 2, 2, 1, 1, 1, 7, 7, 19, 30, 30, 77, 103, 103, 103, 103, 30, 30, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 46, 33, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 581 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580679 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580679 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580679/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580679 Building REAL300025580680 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580680' /scratch/stefan/7787361/working/building/REAL300025580680 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580680 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580680/0 /scratch/stefan/7787361/working/building/REAL300025580680 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/175 `/scratch/stefan/7787361/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(C)NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580680 none CCOC(=O)C1=C(C)NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 171, 110, 171, 110, 110, 110, 110, 61, 61, 61, 19, 8, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 110, 110, 110, 110, 61, 19, 19, 8, 8, 110] 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]) total number of confs: 697 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580680 none CCOC(=O)C1=C(C)NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 6, 6, 7, 24, 30, 110, 110, 110, 110, 110, 1, 16, 16, 16, 16, 16, 2, 2, 2, 1, 7, 24, 24, 30, 30, 1] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 21, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580680 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580680 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580680/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580680 Building REAL300025580681 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580681' /scratch/stefan/7787361/working/building/REAL300025580681 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580681 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580681/0 /scratch/stefan/7787361/working/building/REAL300025580681 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/176 `/scratch/stefan/7787361/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC[C@H](CC(=O)NCCC1=NC(=O)O[N-]1)CC(C)C) `REAL300025580681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580681 none CC(=O)NC[C@H](CC(=O)NCCC1=NC(=O)O[N-]1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 195, 162, 117, 162, 61, 61, 61, 19, 8, 1, 1, 1, 1, 1, 1, 1, 162, 163, 163, 163, 201, 201, 201, 201, 195, 195, 117, 117, 61, 19, 19, 8, 8, 163, 163, 163, 163, 163, 163, 163, 163, 163] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44]) total number of confs: 936 number of broken/clashed sets: 113 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580681 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580681 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580681/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580681 Building REAL300025580682 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580682' /scratch/stefan/7787361/working/building/REAL300025580682 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580682 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580682/0 /scratch/stefan/7787361/working/building/REAL300025580682 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/177 `/scratch/stefan/7787361/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC1C1=CC=C(Cl)C=C1F) `REAL300025580682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580682 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC1C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 32, 32, 96, 102, 201, 201, 201, 201, 201, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 96, 96, 102, 102, 8, 8, 8, 8, 8, 8, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 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]) total number of confs: 561 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: REAL300025580682 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC1C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 58, 65, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 8, 8, 1, 7, 8, 8, 8, 11, 58, 58, 65, 65, 1, 1, 1, 1, 1, 1, 8, 8, 8] 201 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36]) total number of confs: 392 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580682 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC1C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 44, 144, 144, 144, 144, 201, 201, 144, 201, 201, 201, 201, 44, 19, 19, 8, 8, 144, 144, 144, 144, 144, 144, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 755 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580682 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580682 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580682/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580682 Building REAL300025580683 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580683' /scratch/stefan/7787361/working/building/REAL300025580683 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580683 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580683/0 /scratch/stefan/7787361/working/building/REAL300025580683 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/178 `/scratch/stefan/7787361/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025580683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580683 none CCOCC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 183, 89, 89, 89, 89, 89, 39, 39, 39, 15, 7, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 183, 183, 89, 89, 89, 39, 15, 15, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 661 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580683 none CCOCC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 30, 32, 89, 89, 89, 89, 89, 1, 21, 21, 21, 21, 21, 7, 7, 2, 2, 2, 7, 30, 30, 32, 32] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 20] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580683 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580683 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580683/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580683 Building REAL300025580684 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580684' /scratch/stefan/7787361/working/building/REAL300025580684 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580684 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580684/0 /scratch/stefan/7787361/working/building/REAL300025580684 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/179 `/scratch/stefan/7787361/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CCOC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580684 none CC=CCOC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 178, 148, 78, 78, 78, 78, 78, 59, 23, 23, 23, 9, 5, 1, 1, 1, 1, 1, 1, 1, 78, 201, 201, 201, 201, 201, 178, 178, 78, 78, 78, 59, 59, 23, 9, 9, 5, 5, 78] 201 rigid atoms, others: [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: 653 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580684 none CC=CCOC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 8, 6, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 33, 37, 78, 78, 78, 78, 78, 1, 22, 22, 22, 22, 22, 8, 8, 1, 1, 1, 2, 2, 9, 33, 33, 37, 37, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 40, 22, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580684 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580684 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580684/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580684 Building REAL300025580685 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580685' /scratch/stefan/7787361/working/building/REAL300025580685 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580685 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580685/0 /scratch/stefan/7787361/working/building/REAL300025580685 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/180 `/scratch/stefan/7787361/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=NC(Cl)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025580685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580685 none CN(C)C1=NC(Cl)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 201, 190, 190, 190, 190, 74, 74, 74, 19, 8, 1, 1, 1, 1, 1, 1, 1, 190, 201, 201, 201, 201, 201, 201, 73, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 445 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580685 none CN(C)C1=NC(Cl)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 30, 52, 190, 190, 190, 190, 190, 1, 6, 6, 6, 7, 7, 7, 6, 30, 30, 52, 52] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580685 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580685 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580685/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580685 Building REAL300025580686 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580686' /scratch/stefan/7787361/working/building/REAL300025580686 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580686 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580686/0 /scratch/stefan/7787361/working/building/REAL300025580686 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/181 `/scratch/stefan/7787361/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(=O)OCC2=CC=CC=C2)N1) `REAL300025580686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580686 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(=O)OCC2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 71, 71, 139, 139, 201, 201, 201, 201, 201, 43, 43, 43, 23, 19, 23, 4, 1, 1, 1, 1, 1, 1, 1, 43, 71, 139, 139, 140, 140, 43, 43, 4, 4, 1, 1, 1, 1, 1, 43] 201 rigid atoms, others: [35, 36, 37, 38, 39, 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, 40]) total number of confs: 658 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580686 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(=O)OCC2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 18, 21, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 4, 4, 8, 22, 43, 43, 25, 43, 43, 1, 6, 18, 18, 21, 21, 1, 1, 22, 22, 43, 43, 43, 43, 43, 1] 201 rigid atoms, others: [32, 1, 40, 11, 12, 13, 14, 15, 25, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580686 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(=O)OCC2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 1, 1, 1, 1, 1, 1, 1, 33, 53, 53, 53, 53, 79, 79, 87, 201, 201, 201, 201, 201, 201, 53, 33, 15, 15, 7, 7, 53, 53, 201, 201, 201, 201, 201, 201, 201, 53] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 715 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580686 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580686 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580686/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580686 Building REAL300025580687 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580687' /scratch/stefan/7787361/working/building/REAL300025580687 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580687 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580687/0 /scratch/stefan/7787361/working/building/REAL300025580687 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/182 `/scratch/stefan/7787361/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=CC=C2)C1) `REAL300025580687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580687 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 3, 17, 17, 77, 89, 201, 201, 201, 201, 201, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 17, 77, 77, 89, 89, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38]) total number of confs: 505 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580687 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 40, 46, 118, 118, 118, 118, 118, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 9, 40, 40, 46, 46, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1] 201 rigid atoms, others: [1, 37, 38, 11, 12, 13, 14, 15, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36]) total number of confs: 280 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580687 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 20, 8, 1, 1, 1, 1, 1, 1, 1, 59, 118, 118, 118, 118, 201, 201, 201, 201, 201, 118, 59, 20, 20, 8, 8, 118, 118, 118, 118, 118, 201, 201, 201, 201, 201, 118, 118] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 547 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580687 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580687 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580687/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580687 Building REAL300025580688 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580688' /scratch/stefan/7787361/working/building/REAL300025580688 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580688 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580688/0 /scratch/stefan/7787361/working/building/REAL300025580688 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/183 `/scratch/stefan/7787361/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=NN1C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1) `REAL300025580688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580688 none CC1=NN=NN1C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 92, 77, 92, 92, 44, 44, 44, 17, 7, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 201, 201, 201, 92, 92, 44, 17, 17, 7, 7, 92] 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]) total number of confs: 467 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580688 none CC1=NN=NN1C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 44, 47, 92, 92, 92, 92, 92, 1, 1, 1, 9, 9, 9, 1, 1, 12, 44, 44, 47, 47, 1] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 21, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 247 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580688 none CC1=NN=NN1C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 8, 8, 44, 44, 44, 128, 130, 201, 201, 201, 201, 201, 9, 9, 9, 2, 2, 2, 9, 9, 44, 128, 128, 130, 130, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 587 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580688 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580688 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580688/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580688 Building REAL300025580689 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580689' /scratch/stefan/7787361/working/building/REAL300025580689 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580689 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580689/0 /scratch/stefan/7787361/working/building/REAL300025580689 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/184 `/scratch/stefan/7787361/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)C(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580689 none CC(C)C[C@H](NC(=O)C(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 147, 79, 147, 147, 173, 173, 173, 194, 194, 194, 79, 79, 24, 8, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 158, 158, 158, 158, 158, 173, 194, 194, 194, 194, 194, 194, 194, 194, 194, 78, 24, 24, 8, 8] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 860 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580689 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580689 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580689/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580689 Building REAL300025580690 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580690' /scratch/stefan/7787361/working/building/REAL300025580690 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580690 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580690/0 /scratch/stefan/7787361/working/building/REAL300025580690 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/185 `/scratch/stefan/7787361/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(S(=O)(=O)CC2CC2)C=C1)NCCC1=NC(=O)O[N-]1) `REAL300025580690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580690 none O=C(CC1=CC=C(S(=O)(=O)CC2CC2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', '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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 89, 110, 110, 99, 89, 110, 110, 110, 162, 201, 201, 110, 110, 16, 8, 1, 1, 1, 1, 1, 1, 1, 89, 89, 110, 110, 162, 162, 201, 201, 201, 201, 201, 110, 110, 47, 16, 16, 8, 8] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 960 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580690 none O=C(CC1=CC=C(S(=O)(=O)CC2CC2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', '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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 21, 19, 19, 19, 19, 14, 5, 14, 14, 1, 1, 1, 1, 19, 19, 33, 33, 104, 113, 201, 201, 201, 201, 201, 21, 21, 19, 19, 5, 5, 1, 1, 1, 1, 1, 19, 19, 33, 104, 104, 113, 113] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 31] 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 615 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580690 none O=C(CC1=CC=C(S(=O)(=O)CC2CC2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', '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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 1, 1, 7, 7, 35, 41, 110, 110, 110, 110, 110, 4, 4, 1, 1, 12, 12, 19, 19, 19, 19, 19, 1, 1, 7, 35, 35, 41, 41] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 14, 15, 36, 27, 28, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580690 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580690 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580690/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580690 Building REAL300025580691 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580691' /scratch/stefan/7787361/working/building/REAL300025580691 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580691 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580691/0 /scratch/stefan/7787361/working/building/REAL300025580691 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/186 `/scratch/stefan/7787361/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C(F)F)=N1) `REAL300025580691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580691 none CC(C)CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 176, 191, 86, 86, 86, 34, 34, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 86, 86, 121, 121, 86, 191, 191, 191, 191, 191, 191, 191, 176, 176, 86, 33, 8, 8, 8, 8, 121] 201 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, 37, 38]) total number of confs: 893 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580691 none CC(C)CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 7, 1, 1, 1, 1, 1, 6, 6, 6, 25, 25, 86, 86, 86, 86, 86, 1, 1, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 6, 25, 25, 25, 25, 7] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 18, 19, 22] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 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 /scratch/stefan/7787361/working/building/REAL300025580691 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580691 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580691/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580691 Building REAL300025580692 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580692' /scratch/stefan/7787361/working/building/REAL300025580692 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580692 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580692/0 /scratch/stefan/7787361/working/building/REAL300025580692 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/187 `/scratch/stefan/7787361/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1CC(F)(F)F) `REAL300025580692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580692 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1CC(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 5, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 22, 30, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 4, 22, 22, 30, 30, 1, 1, 6, 6] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580692 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1CC(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 5, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 63, 115, 115, 115, 115, 115, 199, 201, 199, 201, 63, 19, 20, 8, 8, 115, 115, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580692 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580692 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580692/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580692 Building REAL300025580693 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580693' /scratch/stefan/7787361/working/building/REAL300025580693 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580693 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580693/0 /scratch/stefan/7787361/working/building/REAL300025580693 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/188 `/scratch/stefan/7787361/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580693 none COC(=O)C1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 95, 201, 201, 95, 39, 39, 39, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 95, 95, 39, 17, 17, 8, 8, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 942 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580693 none COC(=O)C1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 17, 17, 17, 75, 85, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 1, 1, 7, 7, 17, 75, 75, 85, 85, 1, 1] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 34, 20, 21, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580693 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580693 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580693/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580693 Building REAL300025580694 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580694' /scratch/stefan/7787361/working/building/REAL300025580694 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580694 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580694/0 /scratch/stefan/7787361/working/building/REAL300025580694 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/189 `/scratch/stefan/7787361/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OCC1=CC=C(F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580694 none CC(OCC1=CC=C(F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 37, 91, 117, 174, 201, 201, 174, 201, 201, 201, 37, 37, 8, 8, 1, 1, 1, 1, 1, 1, 1, 91, 91, 89, 91, 174, 174, 201, 201, 201, 201, 36, 9, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 869 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580694 none CC(OCC1=CC=C(F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 37, 67, 67, 67, 120, 120, 201, 201, 201, 201, 201, 37, 37, 37, 37, 3, 3, 1, 1, 1, 1, 67, 120, 120, 120, 120] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 625 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580694 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580694 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580694/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580694 Building REAL300025580695 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580695' /scratch/stefan/7787361/working/building/REAL300025580695 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580695 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580695/0 /scratch/stefan/7787361/working/building/REAL300025580695 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/190 `/scratch/stefan/7787361/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=C(Br)C=C1F) `REAL300025580695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580695 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=C(Br)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 17, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 68, 100, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 68, 68, 100, 100, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 572 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580695 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=C(Br)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 17, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 90, 22, 8, 1, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 201, 201, 201, 201, 201, 90, 22, 22, 8, 8, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 443 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580695 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580695 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580695/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580695 Building REAL300025580696 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580696' /scratch/stefan/7787361/working/building/REAL300025580696 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580696 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580696/0 /scratch/stefan/7787361/working/building/REAL300025580696 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/191 `/scratch/stefan/7787361/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C1=CC=C2C=C(C(=O)NCCC3=NC(=O)O[N-]3)C(=O)OC2=C1) `REAL300025580696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580696 none CCN(CC)C1=CC=C2C=C(C(=O)NCCC3=NC(=O)O[N-]3)C(=O)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 112, 68, 112, 158, 68, 68, 68, 68, 68, 47, 47, 47, 18, 8, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 164, 164, 164, 164, 164, 158, 158, 158, 158, 158, 68, 68, 68, 47, 18, 18, 8, 8, 68] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 953 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580696 none CCN(CC)C1=CC=C2C=C(C(=O)NCCC3=NC(=O)O[N-]3)C(=O)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 3, 1, 3, 9, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 28, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 1, 1, 1, 8, 26, 26, 28, 28, 1] 201 rigid atoms, others: [2, 11, 37, 6, 7, 8, 9, 10, 39, 45, 22, 23, 24, 25, 26, 38, 5] set([0, 1, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580696 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580696 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580696/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580696 Building REAL300025580697 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580697' /scratch/stefan/7787361/working/building/REAL300025580697 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580697 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580697/0 /scratch/stefan/7787361/working/building/REAL300025580697 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/192 `/scratch/stefan/7787361/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(I)C=C1F) `REAL300025580697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580697 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(I)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 18, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [12, 1, 12, 13, 71, 114, 199, 199, 199, 199, 199, 1, 1, 1, 1, 1, 1, 1, 1, 13, 71, 71, 114, 114, 1, 1, 1] 199 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 630 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580697 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(I)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 18, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [109, 109, 24, 8, 1, 1, 1, 1, 1, 1, 1, 109, 199, 199, 151, 199, 199, 199, 199, 109, 25, 25, 8, 8, 199, 199, 199] 199 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 655 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580697 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580697 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580697/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580697 Building REAL300025580698 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580698' /scratch/stefan/7787361/working/building/REAL300025580698 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580698 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580698/0 /scratch/stefan/7787361/working/building/REAL300025580698 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/193 `/scratch/stefan/7787361/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=C(F)C=C1Br) `REAL300025580698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580698 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=C(F)C=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 15, 1, 1, 17, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 43, 59, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 43, 43, 59, 59, 1, 1] 151 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580698 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=C(F)C=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 15, 1, 1, 17, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 20, 8, 1, 1, 1, 1, 1, 1, 1, 76, 151, 151, 151, 151, 151, 151, 151, 151, 76, 21, 21, 8, 8, 151, 151] 151 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580698 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580698 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580698/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580698 Building REAL300025580699 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580699' /scratch/stefan/7787361/working/building/REAL300025580699 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580699 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580699/0 /scratch/stefan/7787361/working/building/REAL300025580699 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/194 `/scratch/stefan/7787361/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C(F)(F)F)=CC=C1[N+](=O)[O-]) `REAL300025580699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580699 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C(F)(F)F)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 27, 44, 85, 85, 85, 85, 85, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 7, 27, 27, 44, 44, 1, 1, 1] 85 rigid atoms, others: [1, 11, 12, 13, 14, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580699 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C(F)(F)F)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [59, 59, 21, 8, 1, 1, 1, 1, 1, 1, 1, 59, 85, 85, 85, 85, 85, 85, 59, 85, 85, 85, 85, 85, 59, 21, 21, 8, 8, 85, 59, 85] 85 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580699 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580699 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580699/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580699 Building REAL300025580700 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580700' /scratch/stefan/7787361/working/building/REAL300025580700 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580700 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580700/0 /scratch/stefan/7787361/working/building/REAL300025580700 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/195 `/scratch/stefan/7787361/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(CCN2C=CC=N2)C=C1) `REAL300025580700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580700 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(CCN2C=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 8, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 25, 40, 40, 101, 122, 201, 201, 201, 201, 201, 25, 25, 10, 6, 1, 1, 1, 1, 1, 1, 25, 25, 40, 101, 101, 122, 122, 10, 10, 6, 6, 1, 1, 1, 25, 25] 201 rigid atoms, others: [32, 33, 34, 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, 35, 36]) total number of confs: 625 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580700 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(CCN2C=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 8, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 18, 23, 75, 75, 75, 75, 75, 1, 1, 1, 1, 6, 10, 25, 25, 25, 25, 1, 1, 5, 18, 18, 23, 23, 6, 6, 10, 10, 25, 25, 25, 1, 1] 201 rigid atoms, others: [1, 35, 36, 11, 12, 13, 14, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580700 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(CCN2C=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 8, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 8, 1, 1, 1, 1, 1, 1, 1, 57, 75, 75, 75, 150, 182, 201, 201, 201, 201, 75, 75, 57, 22, 22, 8, 8, 150, 150, 182, 182, 201, 201, 201, 75, 75] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 808 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580700 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580700 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580700/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580700 Building REAL300025580701 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580701' /scratch/stefan/7787361/working/building/REAL300025580701 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580701 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580701/0 /scratch/stefan/7787361/working/building/REAL300025580701 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/196 `/scratch/stefan/7787361/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@H]1CCCN1C(=O)C1=CC=CC=C1) `REAL300025580701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580701 none O=C(NCCC1=NC(=O)O[N-]1)[C@H]1CCCN1C(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 10, 30, 30, 89, 107, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 30, 89, 89, 107, 107, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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]) total number of confs: 585 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580701 none O=C(NCCC1=NC(=O)O[N-]1)[C@H]1CCCN1C(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 29, 44, 136, 136, 136, 136, 136, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 7, 10, 10, 6, 29, 29, 44, 44, 1, 1, 1, 1, 1, 1, 10, 10, 7, 10, 10] 201 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40]) total number of confs: 333 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580701 none O=C(NCCC1=NC(=O)O[N-]1)[C@H]1CCCN1C(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 89, 136, 136, 136, 136, 136, 136, 201, 201, 201, 201, 201, 201, 201, 88, 24, 24, 8, 8, 136, 136, 136, 136, 136, 136, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 670 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580701 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580701 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580701/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580701 Building REAL300025580702 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580702' /scratch/stefan/7787361/working/building/REAL300025580702 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580702 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580702/0 /scratch/stefan/7787361/working/building/REAL300025580702 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/197 `/scratch/stefan/7787361/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCC1C1=CC=CC=C1) `REAL300025580702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580702 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 4, 23, 23, 96, 107, 201, 201, 201, 201, 201, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 23, 96, 96, 107, 107, 4, 4, 4, 4, 4, 4, 4, 4, 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: 554 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580702 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 49, 63, 158, 158, 158, 158, 158, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 10, 49, 49, 63, 63, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4] 201 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38, 39]) total number of confs: 391 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580702 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 22, 8, 1, 1, 1, 1, 1, 1, 1, 67, 158, 158, 158, 158, 158, 201, 201, 158, 201, 201, 67, 23, 22, 8, 8, 158, 158, 158, 158, 158, 158, 158, 158, 201, 201, 158, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 650 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580702 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580702 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580702/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580702 Building REAL300025580703 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580703' /scratch/stefan/7787361/working/building/REAL300025580703 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580703 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580703/0 /scratch/stefan/7787361/working/building/REAL300025580703 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/198 `/scratch/stefan/7787361/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(CCC2=CC=CC=C2)C=C1) `REAL300025580703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580703 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(CCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 12, 22, 22, 74, 101, 201, 201, 201, 201, 201, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 22, 74, 74, 101, 101, 3, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39]) total number of confs: 585 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580703 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(CCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 25, 85, 85, 85, 85, 85, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 12, 1, 1, 4, 16, 16, 25, 25, 8, 8, 12, 12, 12, 12, 12, 12, 12, 1, 1] 201 rigid atoms, others: [1, 38, 39, 11, 12, 13, 14, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580703 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(CCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 24, 8, 1, 1, 1, 1, 1, 1, 1, 74, 85, 85, 85, 182, 201, 201, 201, 201, 201, 201, 85, 85, 74, 24, 24, 8, 8, 182, 182, 201, 201, 201, 201, 201, 201, 201, 85, 85] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 825 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580703 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580703 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580703/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580703 Building REAL300025580704 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580704' /scratch/stefan/7787361/working/building/REAL300025580704 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580704 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580704/0 /scratch/stefan/7787361/working/building/REAL300025580704 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/199 `/scratch/stefan/7787361/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C(=O)C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)[C@H]1C1=CC=CN=C1) `REAL300025580704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580704 none CCN1C(=O)C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)[C@H]1C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 76, 83, 172, 172, 172, 172, 172, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 7, 7, 25, 76, 76, 83, 83, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 471 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580704 none CCN1C(=O)C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)[C@H]1C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 110, 110, 110, 110, 110, 44, 110, 44, 44, 18, 9, 1, 1, 1, 1, 1, 1, 1, 110, 110, 110, 172, 172, 172, 172, 172, 134, 134, 134, 134, 134, 110, 110, 44, 18, 18, 9, 9, 172, 172, 172, 172] 201 rigid atoms, others: [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, 39, 40, 41, 42]) total number of confs: 613 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580704 none CCN1C(=O)C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)[C@H]1C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 38, 44, 110, 110, 110, 110, 110, 1, 1, 1, 7, 7, 7, 7, 7, 3, 3, 3, 2, 2, 1, 1, 8, 38, 38, 44, 44, 7, 7, 7, 7] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 7, 19, 20, 21] set([0, 9, 10, 11, 12, 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]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580704 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580704 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580704/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580704 Building REAL300025580705 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580705' /scratch/stefan/7787361/working/building/REAL300025580705 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580705 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580705/0 /scratch/stefan/7787361/working/building/REAL300025580705 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/200 `/scratch/stefan/7787361/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(=O)OC)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580705 none CC[C@H](C)[C@H](NC(=O)OC)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 146, 110, 148, 139, 40, 116, 116, 143, 183, 183, 183, 40, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 150, 148, 148, 148, 143, 183, 183, 183, 39, 9, 9, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 938 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580705 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580705 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580705/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580705 Building REAL300025580706 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580706' /scratch/stefan/7787361/working/building/REAL300025580706 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580706 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580706/0 /scratch/stefan/7787361/working/building/REAL300025580706 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/201 `/scratch/stefan/7787361/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCCC[C@@H]1C1=CC=CC=C1) `REAL300025580706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580706 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCCC[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 7, 30, 42, 105, 105, 105, 105, 105, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 30, 30, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 105 rigid atoms, others: [38, 39, 40, 41, 42, 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]) total number of confs: 271 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580706 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCCC[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 24, 36, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 6, 24, 24, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3] 105 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580706 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCCC[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 23, 9, 1, 1, 1, 1, 1, 1, 1, 73, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 73, 23, 23, 8, 8, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105] 105 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580706 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580706 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580706/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580706 Building REAL300025580707 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580707' /scratch/stefan/7787361/working/building/REAL300025580707 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580707 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580707/0 /scratch/stefan/7787361/working/building/REAL300025580707 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/202 `/scratch/stefan/7787361/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1COCCN1C(=O)OCC1=CC=CC=C1) `REAL300025580707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580707 none O=C(NCCC1=NC(=O)O[N-]1)C1COCCN1C(=O)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 38, 38, 99, 102, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 24, 15, 24, 4, 1, 1, 1, 1, 1, 1, 1, 38, 99, 99, 102, 102, 30, 30, 30, 30, 30, 30, 30, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 535 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580707 none O=C(NCCC1=NC(=O)O[N-]1)C1COCCN1C(=O)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 12, 14, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 19, 30, 30, 27, 30, 30, 3, 12, 12, 14, 14, 1, 1, 1, 1, 1, 1, 1, 19, 19, 30, 30, 30, 30, 30] 201 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 11, 12, 13, 14, 15, 16, 17] set([0, 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, 41, 42, 43, 44, 45]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580707 none O=C(NCCC1=NC(=O)O[N-]1)C1COCCN1C(=O)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 8, 1, 1, 1, 1, 1, 1, 1, 49, 60, 60, 60, 60, 60, 60, 80, 80, 91, 201, 201, 201, 201, 201, 201, 49, 18, 18, 8, 8, 60, 60, 60, 60, 60, 60, 60, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 794 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580707 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580707 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580707/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580707 Building REAL300025580708 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580708' /scratch/stefan/7787361/working/building/REAL300025580708 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580708 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580708/0 /scratch/stefan/7787361/working/building/REAL300025580708 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/203 `/scratch/stefan/7787361/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)OC(C)(C)C)C(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580708 none CCCN(C(=O)OC(C)(C)C)C(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 110, 85, 110, 161, 161, 163, 163, 163, 163, 34, 85, 34, 34, 13, 7, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 138, 138, 138, 163, 163, 163, 163, 163, 163, 163, 163, 163, 85, 85, 85, 85, 34, 13, 13, 7, 7] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 787 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580708 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580708 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580708/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580708 Building REAL300025580709 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580709' /scratch/stefan/7787361/working/building/REAL300025580709 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580709 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580709/0 /scratch/stefan/7787361/working/building/REAL300025580709 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/204 `/scratch/stefan/7787361/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(NC2CC2)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580709 none CC1=NSC(NC2CC2)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 8, 5, 5, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 126, 139, 139, 139, 139, 139, 201, 201, 66, 66, 66, 17, 8, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 201, 201, 201, 201, 201, 66, 17, 17, 8, 8] 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]) total number of confs: 603 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580709 none CC1=NSC(NC2CC2)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 8, 5, 5, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 9, 1, 1, 1, 1, 20, 20, 36, 36, 36, 107, 114, 201, 201, 201, 201, 201, 20, 20, 20, 9, 1, 1, 1, 1, 1, 36, 107, 107, 114, 114] 201 rigid atoms, others: [5, 6, 7, 8, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34]) total number of confs: 567 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580709 none CC1=NSC(NC2CC2)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 8, 5, 5, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 20, 20, 1, 1, 7, 7, 7, 39, 44, 139, 139, 139, 139, 139, 2, 2, 2, 3, 20, 20, 20, 20, 20, 7, 39, 39, 44, 44] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 345 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580709 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580709 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580709/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580709 Building REAL300025580710 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580710' /scratch/stefan/7787361/working/building/REAL300025580710 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580710 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580710/0 /scratch/stefan/7787361/working/building/REAL300025580710 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/205 `/scratch/stefan/7787361/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC(F)=C2N=C1) `REAL300025580710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580710 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC(F)=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 48, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 48, 48, 1, 1, 1, 1, 1] 103 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580710 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC(F)=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 24, 8, 1, 1, 1, 1, 1, 1, 1, 53, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 52, 24, 24, 8, 8, 103, 103, 103, 103, 103] 103 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580710 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580710 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580710/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580710 Building REAL300025580711 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580711' /scratch/stefan/7787361/working/building/REAL300025580711 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580711 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580711/0 /scratch/stefan/7787361/working/building/REAL300025580711 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/206 `/scratch/stefan/7787361/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC=C(Cl)C=C2)=C1) `REAL300025580711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580711 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 25, 92, 98, 201, 201, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 25, 92, 92, 98, 98, 6, 1, 1, 1, 1, 7] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 518 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580711 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 37, 132, 132, 132, 132, 132, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 6, 1, 5, 29, 29, 37, 37, 1, 7, 7, 7, 7, 1] 201 rigid atoms, others: [1, 33, 11, 12, 13, 14, 15, 22, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580711 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 55, 132, 127, 132, 132, 201, 201, 201, 201, 201, 201, 132, 55, 19, 19, 8, 8, 132, 201, 201, 201, 201, 132] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 456 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580711 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580711 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580711/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580711 Building REAL300025580712 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580712' /scratch/stefan/7787361/working/building/REAL300025580712 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580712 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580712/0 /scratch/stefan/7787361/working/building/REAL300025580712 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/207 `/scratch/stefan/7787361/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)C)C(C)=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580712 none CC1=NN(C(C)C)C(C)=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 49, 49, 49, 15, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 152, 49, 15, 15, 8, 8] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 674 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580712 none CC1=NN(C(C)C)C(C)=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 4, 25, 24, 25, 85, 91, 201, 201, 201, 201, 201, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 4, 4, 24, 85, 85, 91, 91] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/7787361/working/building/REAL300025580712 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580712 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580712/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580712 Building REAL300025580713 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580713' /scratch/stefan/7787361/working/building/REAL300025580713 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580713 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580713/0 /scratch/stefan/7787361/working/building/REAL300025580713 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/208 `/scratch/stefan/7787361/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)OC(=O)C2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC=C21) `REAL300025580713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580713 none CC1(C)OC(=O)C2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 159, 159, 159, 159, 97, 97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 159, 159, 159, 159, 159, 97, 24, 24, 8, 8, 159, 159, 159] 159 rigid atoms, others: [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]) total number of confs: 397 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580713 none CC1(C)OC(=O)C2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 61, 91, 159, 159, 159, 159, 159, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 11, 61, 61, 91, 91, 1, 1, 1] 159 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 19, 20, 21, 22, 36, 35] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 501 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580713 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580713 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580713/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580713 Building REAL300025580714 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580714' /scratch/stefan/7787361/working/building/REAL300025580714 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580714 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580714/0 /scratch/stefan/7787361/working/building/REAL300025580714 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/209 `/scratch/stefan/7787361/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC=C(C(F)(F)F)C=C2)C1) `REAL300025580714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580714 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC=C(C(F)(F)F)C=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 5, 31, 31, 103, 106, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 31, 103, 103, 106, 106, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 551 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580714 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC=C(C(F)(F)F)C=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 54, 63, 139, 139, 139, 139, 139, 1, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 5, 5, 1, 11, 54, 54, 63, 63, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [32, 1, 38, 33, 11, 12, 13, 14, 24, 39, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 385 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580714 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC=C(C(F)(F)F)C=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 19, 8, 1, 1, 1, 1, 1, 1, 1, 61, 139, 139, 139, 201, 201, 139, 154, 201, 201, 201, 201, 201, 139, 61, 19, 19, 8, 8, 139, 139, 139, 139, 201, 201, 201, 201, 139, 139] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1046 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580714 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580714 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580714/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580714 Building REAL300025580715 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580715' /scratch/stefan/7787361/working/building/REAL300025580715 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580715 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580715/0 /scratch/stefan/7787361/working/building/REAL300025580715 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/210 `/scratch/stefan/7787361/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(F)(F)F)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580715 none COC1=CC(C(F)(F)F)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 152, 201, 201, 201, 201, 201, 201, 65, 65, 65, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 64, 20, 20, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 593 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580715 none COC1=CC(C(F)(F)F)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 12, 12, 12, 65, 77, 201, 201, 201, 201, 201, 3, 3, 3, 1, 1, 1, 12, 65, 65, 77, 77] 201 rigid atoms, others: [1, 2, 3, 4, 5, 9, 10, 11, 12, 26, 27, 28] set([0, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580715 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580715 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580715/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580715 Building REAL300025580716 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580716' /scratch/stefan/7787361/working/building/REAL300025580716 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580716 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580716/0 /scratch/stefan/7787361/working/building/REAL300025580716 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/211 `/scratch/stefan/7787361/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(Br)C=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025580716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580716 none CCC1=C(Br)C=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 116, 116, 116, 116, 116, 76, 76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 116, 199, 201, 201, 201, 201, 116, 76, 24, 24, 8, 8] 201 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]) total number of confs: 827 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580716 none CCC1=C(Br)C=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 42, 51, 116, 116, 116, 116, 116, 1, 6, 6, 6, 5, 5, 1, 9, 42, 42, 51, 51] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 18, 24] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580716 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580716 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580716/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580716 Building REAL300025580717 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580717' /scratch/stefan/7787361/working/building/REAL300025580717 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580717 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580717/0 /scratch/stefan/7787361/working/building/REAL300025580717 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/212 `/scratch/stefan/7787361/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL300025580717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580717 none CC(C)(C)OC(=O)N[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 17, 10, 17, 4, 1, 4, 4, 13, 13, 13, 40, 40, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 13, 40, 40, 40, 40, 1, 1, 1, 1, 1] 201 rigid atoms, others: [8, 42, 43, 44, 45, 46, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 311 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580717 none CC(C)(C)OC(=O)N[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 182, 131, 182, 87, 35, 87, 35, 35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 87, 114, 114, 113, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 34, 8, 8, 8, 8, 114, 114, 114, 114, 114] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 779 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580717 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580717 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580717/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580717 Building REAL300025580718 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580718' /scratch/stefan/7787361/working/building/REAL300025580718 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580718 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580718/0 /scratch/stefan/7787361/working/building/REAL300025580718 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/213 `/scratch/stefan/7787361/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL300025580718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580718 none CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 17, 10, 17, 4, 1, 4, 13, 13, 13, 41, 41, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 4, 13, 41, 41, 41, 41, 1, 1, 1, 1, 1] 201 rigid atoms, others: [8, 42, 43, 44, 45, 46, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 320 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580718 none CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 181, 133, 181, 90, 34, 34, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 90, 116, 116, 97, 116, 116, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 90, 33, 8, 8, 8, 8, 116, 116, 116, 116, 116] 201 rigid atoms, others: [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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 870 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580718 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580718 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580718/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580718 Building REAL300025580719 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580719' /scratch/stefan/7787361/working/building/REAL300025580719 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580719 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580719/0 /scratch/stefan/7787361/working/building/REAL300025580719 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/214 `/scratch/stefan/7787361/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)C=C1) `REAL300025580719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580719 none CN(C)C1=CC=C(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 201, 174, 185, 185, 174, 69, 69, 69, 23, 8, 1, 1, 1, 1, 1, 1, 1, 174, 174, 185, 185, 201, 201, 201, 201, 201, 201, 185, 185, 69, 23, 23, 8, 8, 174, 174, 174, 174, 185, 185] 201 rigid atoms, others: [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, 39, 40, 41]) total number of confs: 689 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580719 none CN(C)C1=CC=C(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 4, 4, 1, 1, 1, 12, 12, 12, 50, 61, 174, 174, 174, 174, 174, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 4, 4, 12, 50, 50, 61, 61, 1, 1, 1, 1, 4, 4] 201 rigid atoms, others: [36, 37, 6, 7, 8, 39, 19, 20, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 415 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580719 none CN(C)C1=CC=C(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 4, 16, 16, 16, 69, 76, 188, 188, 188, 188, 188, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 16, 69, 69, 76, 76, 4, 4, 4, 4, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 21, 22, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 450 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580719 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580719 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580719/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580719 Building REAL300025580720 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580720' /scratch/stefan/7787361/working/building/REAL300025580720 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580720 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580720/0 /scratch/stefan/7787361/working/building/REAL300025580720 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/215 `/scratch/stefan/7787361/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CSC=C1Br)NCCC1=NC(=O)O[N-]1) `REAL300025580720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580720 none O=C(CC1=CSC=C1Br)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Br', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 1, 17, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 114, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 114, 114, 201, 201, 41, 17, 17, 8, 8] 201 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]) total number of confs: 579 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580720 none O=C(CC1=CSC=C1Br)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Br', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 1, 17, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 6, 1, 1, 1, 1, 1, 1, 1, 34, 34, 117, 117, 201, 201, 201, 201, 201, 6, 6, 1, 1, 34, 117, 117, 117, 117] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26]) total number of confs: 588 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580720 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580720 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580720/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580720 Building REAL300025580721 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580721' /scratch/stefan/7787361/working/building/REAL300025580721 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580721 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580721/0 /scratch/stefan/7787361/working/building/REAL300025580721 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/216 `/scratch/stefan/7787361/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CCC2=CC=CC=C2)N=N1) `REAL300025580721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580721 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CCC2=CC=CC=C2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 10, 33, 33, 87, 111, 201, 201, 201, 201, 201, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 87, 87, 111, 111, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 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]) total number of confs: 581 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580721 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CCC2=CC=CC=C2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 22, 30, 121, 121, 121, 122, 122, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 1, 1, 6, 21, 21, 30, 30, 1, 8, 8, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [1, 11, 12, 13, 14, 22, 23, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580721 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CCC2=CC=CC=C2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 24, 8, 1, 1, 1, 1, 1, 1, 1, 80, 122, 122, 122, 199, 201, 201, 201, 201, 201, 201, 121, 121, 79, 24, 24, 8, 8, 122, 199, 199, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 757 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580721 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580721 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580721/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580721 Building REAL300025580722 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580722' /scratch/stefan/7787361/working/building/REAL300025580722 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580722 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580722/0 /scratch/stefan/7787361/working/building/REAL300025580722 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/217 `/scratch/stefan/7787361/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C(=C1)NC(=O)CNC2=O) `REAL300025580722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580722 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C(=C1)NC(=O)CNC2=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 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: [7, 1, 7, 7, 39, 62, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 62, 62, 1, 1, 1, 1, 1, 1, 1] 137 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28]) total number of confs: 373 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580722 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C(=C1)NC(=O)CNC2=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 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: [68, 67, 20, 8, 1, 1, 1, 1, 1, 1, 1, 68, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 67, 20, 20, 8, 8, 137, 137, 137, 137, 137, 137, 137] 137 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580722 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580722 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580722/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580722 Building REAL300025580723 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580723' /scratch/stefan/7787361/working/building/REAL300025580723 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580723 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580723/0 /scratch/stefan/7787361/working/building/REAL300025580723 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/218 `/scratch/stefan/7787361/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CC(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Br) `REAL300025580723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580723 none CC1=CC(CC(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 76, 33, 76, 76, 33, 33, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 104, 104, 76, 76, 76, 76, 76, 76, 33, 17, 17, 8, 8, 201, 201] 201 rigid atoms, others: [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, 39, 40, 41]) total number of confs: 675 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580723 none CC1=CC(CC(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 14, 14, 14, 29, 30, 29, 103, 107, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 15, 15, 15, 15, 15, 15, 30, 103, 103, 107, 107, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 40, 41, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 598 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580723 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580723 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580723/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580723 Building REAL300025580724 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580724' /scratch/stefan/7787361/working/building/REAL300025580724 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580724 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580724/0 /scratch/stefan/7787361/working/building/REAL300025580724 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/219 `/scratch/stefan/7787361/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC2=CC=CC=C21) `REAL300025580724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580724 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 9, 9, 9, 49, 81, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 9, 49, 49, 81, 81, 1, 1, 1, 1, 1, 1, 1] 178 rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 503 number of broken/clashed sets: 178 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580724 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 90, 178, 90, 90, 22, 8, 1, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 90, 22, 22, 8, 8, 178, 178, 178, 178, 178, 178, 178] 178 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 670 number of broken/clashed sets: 178 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580724 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580724 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580724/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580724 Building REAL300025580725 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580725' /scratch/stefan/7787361/working/building/REAL300025580725 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580725 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580725/0 /scratch/stefan/7787361/working/building/REAL300025580725 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/220 `/scratch/stefan/7787361/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC(Br)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580725 none CN(C)C1=CC(Br)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 201, 189, 189, 189, 189, 189, 65, 65, 65, 19, 8, 1, 1, 1, 1, 1, 1, 1, 189, 201, 201, 201, 201, 201, 201, 189, 189, 65, 19, 19, 8, 8, 189] 201 rigid atoms, others: [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: 430 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580725 none CN(C)C1=CC(Br)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 39, 189, 189, 189, 189, 189, 1, 5, 5, 5, 5, 5, 5, 1, 1, 5, 29, 29, 39, 39, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 20, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 339 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580725 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580725 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580725/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580725 Building REAL300025580726 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580726' /scratch/stefan/7787361/working/building/REAL300025580726 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580726 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580726/0 /scratch/stefan/7787361/working/building/REAL300025580726 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/221 `/scratch/stefan/7787361/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC(C#N)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580726 none CN(C)C1=CC(C#N)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 201, 187, 187, 187, 187, 187, 187, 73, 73, 73, 23, 8, 1, 1, 1, 1, 1, 1, 1, 187, 201, 201, 201, 201, 201, 201, 187, 187, 73, 23, 23, 8, 8, 187] 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]) total number of confs: 456 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580726 none CN(C)C1=CC(C#N)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 40, 187, 187, 187, 187, 187, 1, 6, 6, 6, 6, 6, 6, 1, 1, 5, 29, 29, 40, 40, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 35, 21, 28, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 350 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580726 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580726 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580726/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580726 Building REAL300025580727 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580727' /scratch/stefan/7787361/working/building/REAL300025580727 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580727 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580727/0 /scratch/stefan/7787361/working/building/REAL300025580727 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/222 `/scratch/stefan/7787361/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C1=NN(C)C=C1) `REAL300025580727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580727 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C1=NN(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 18, 18, 18, 62, 92, 182, 182, 182, 182, 182, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 18, 62, 62, 92, 92, 2, 2, 2, 1, 1] 182 rigid atoms, others: [34, 35, 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]) total number of confs: 524 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580727 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C1=NN(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 101, 101, 101, 24, 8, 1, 1, 1, 1, 1, 1, 1, 182, 182, 182, 182, 182, 182, 182, 182, 182, 182, 182, 182, 100, 25, 24, 8, 8, 182, 182, 182, 182, 182] 182 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 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: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580727 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C1=NN(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 10, 54, 84, 182, 182, 182, 182, 182, 1, 1, 1, 1, 4, 4, 4, 4, 4, 2, 2, 2, 10, 54, 54, 84, 84, 4, 4, 4, 4, 4] 182 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17] set([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, 34, 35]) total number of confs: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580727 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580727 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580727/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580727 Building REAL300025580728 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580728' /scratch/stefan/7787361/working/building/REAL300025580728 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580728 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580728/0 /scratch/stefan/7787361/working/building/REAL300025580728 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/223 `/scratch/stefan/7787361/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1C(F)(F)F) `REAL300025580728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580728 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 25, 42, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 25, 25, 42, 42, 1, 1, 1] 88 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580728 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 23, 8, 1, 1, 1, 1, 1, 1, 1, 63, 88, 88, 88, 88, 88, 63, 88, 88, 88, 88, 88, 88, 63, 23, 23, 8, 8, 88, 63, 88] 88 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580728 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580728 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580728/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580728 Building REAL300025580729 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580729' /scratch/stefan/7787361/working/building/REAL300025580729 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580729 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580729/0 /scratch/stefan/7787361/working/building/REAL300025580729 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/224 `/scratch/stefan/7787361/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(=O)N1CCN(C2=CC=CC=C2)CC1) `REAL300025580729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580729 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)N1CCN(C2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 38, 38, 102, 111, 201, 201, 201, 201, 201, 5, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 38, 102, 102, 111, 111, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40, 41, 42]) total number of confs: 582 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580729 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)N1CCN(C2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 29, 29, 90, 99, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 5, 5, 3, 5, 5, 1, 1, 29, 90, 90, 99, 99, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 566 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580729 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)N1CCN(C2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 63, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 63, 19, 19, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 533 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580729 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580729 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580729/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580729 Building REAL300025580730 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580730' /scratch/stefan/7787361/working/building/REAL300025580730 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580730 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580730/0 /scratch/stefan/7787361/working/building/REAL300025580730 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/225 `/scratch/stefan/7787361/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=C(F)C=C2)CCOCC1) `REAL300025580730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580730 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=C(F)C=C2)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 10, 13, 13, 73, 97, 201, 201, 201, 201, 201, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 13, 73, 73, 97, 97, 2, 2, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10] 201 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, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 568 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580730 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=C(F)C=C2)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 27, 123, 123, 123, 123, 123, 1, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 15, 15, 27, 27, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580730 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=C(F)C=C2)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 22, 8, 1, 1, 1, 1, 1, 1, 1, 72, 123, 201, 201, 201, 201, 201, 201, 201, 123, 123, 123, 123, 123, 72, 22, 22, 8, 8, 201, 201, 201, 201, 201, 201, 123, 123, 123, 123, 123, 123, 123, 123] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 860 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580730 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580730 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580730/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580730 Building REAL300025580731 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580731' /scratch/stefan/7787361/working/building/REAL300025580731 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580731 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580731/0 /scratch/stefan/7787361/working/building/REAL300025580731 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/226 `/scratch/stefan/7787361/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Br)C=C2)C=C1) `REAL300025580731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580731 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 3, 27, 27, 74, 94, 163, 163, 163, 163, 163, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 27, 74, 74, 94, 94, 1, 1, 1, 1, 4, 3] 163 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 32, 33]) total number of confs: 484 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580731 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 1, 13, 13, 57, 82, 163, 163, 163, 163, 163, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 1, 13, 57, 57, 82, 82, 4, 4, 4, 4, 1, 1] 163 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 478 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580731 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [96, 96, 24, 8, 1, 1, 1, 1, 1, 1, 1, 96, 163, 163, 163, 163, 163, 163, 163, 163, 163, 163, 163, 96, 24, 24, 8, 8, 163, 163, 163, 163, 163, 163] 163 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580731 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580731 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580731/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580731 Building REAL300025580732 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580732' /scratch/stefan/7787361/working/building/REAL300025580732 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580732 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580732/0 /scratch/stefan/7787361/working/building/REAL300025580732 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/227 `/scratch/stefan/7787361/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C(=O)CCCC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580732 none COC1=CC=CC(C(=O)CCCC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 169, 114, 169, 84, 106, 53, 53, 53, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 111, 111, 106, 106, 106, 106, 53, 15, 15, 7, 7, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 820 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580732 none COC1=CC=CC(C(=O)CCCC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 22, 23, 37, 37, 37, 108, 110, 201, 201, 201, 201, 201, 1, 3, 3, 3, 1, 1, 1, 17, 17, 21, 21, 23, 23, 37, 108, 108, 110, 110, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 41, 23, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 628 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580732 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580732 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580732/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580732 Building REAL300025580733 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580733' /scratch/stefan/7787361/working/building/REAL300025580733 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580733 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580733/0 /scratch/stefan/7787361/working/building/REAL300025580733 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/228 `/scratch/stefan/7787361/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C(F)(F)F)=N1) `REAL300025580733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580733 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 5, 15, 15, 15, 8, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 97, 97, 97, 21, 8, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 177, 177, 177, 177, 177, 96, 21, 22, 8, 8] 177 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 408 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580733 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 5, 15, 15, 15, 8, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 9, 9, 9, 57, 90, 177, 177, 177, 177, 177, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 57, 57, 90, 90] 177 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 530 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580733 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580733 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580733/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580733 Building REAL300025580734 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580734' /scratch/stefan/7787361/working/building/REAL300025580734 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580734 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580734/0 /scratch/stefan/7787361/working/building/REAL300025580734 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/229 `/scratch/stefan/7787361/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(Br)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580734 none COC(=O)C1=CC(Br)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 130, 201, 130, 130, 130, 130, 130, 51, 51, 51, 17, 8, 1, 1, 1, 1, 1, 1, 1, 130, 201, 201, 201, 130, 130, 51, 17, 17, 8, 8, 130] 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]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580734 none COC(=O)C1=CC(Br)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 33, 130, 130, 130, 130, 130, 1, 11, 11, 11, 1, 1, 5, 29, 29, 33, 33, 1] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 21, 25, 26] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580734 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580734 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580734/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580734 Building REAL300025580735 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580735' /scratch/stefan/7787361/working/building/REAL300025580735 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580735 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580735/0 /scratch/stefan/7787361/working/building/REAL300025580735 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/230 `/scratch/stefan/7787361/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CNC2=CC=CC(Cl)=C12)NCCC1=NC(=O)O[N-]1) `REAL300025580735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580735 none O=C(CC1=CNC2=CC=CC(Cl)=C12)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 15, 7, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 201, 201, 201, 39, 15, 15, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 584 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580735 none O=C(CC1=CNC2=CC=CC(Cl)=C12)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 114, 114, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 35, 114, 114, 114, 114] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28] set([0, 1, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580735 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580735 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580735/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580735 Building REAL300025580736 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580736' /scratch/stefan/7787361/working/building/REAL300025580736 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580736 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580736/0 /scratch/stefan/7787361/working/building/REAL300025580736 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/231 `/scratch/stefan/7787361/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1OC) `REAL300025580736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580736 none COC1=CC(Br)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 148, 148, 148, 148, 148, 60, 60, 60, 17, 8, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 201, 201, 201, 201, 148, 60, 17, 17, 8, 8, 148, 201, 201, 201] 201 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]) total number of confs: 518 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580736 none COC1=CC(Br)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 41, 148, 148, 148, 148, 148, 1, 1, 1, 3, 4, 4, 4, 1, 7, 39, 39, 41, 41, 1, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 25, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 26, 27, 28, 29, 30, 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 /scratch/stefan/7787361/working/building/REAL300025580736 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580736 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580736/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580736 Building REAL300025580737 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580737' /scratch/stefan/7787361/working/building/REAL300025580737 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580737 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580737/0 /scratch/stefan/7787361/working/building/REAL300025580737 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/232 `/scratch/stefan/7787361/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CN=C1C(F)(F)F) `REAL300025580737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580737 none N#CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CN=C1C(F)(F)F NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 5, 15, 15, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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, 135, 60, 60, 60, 20, 8, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 135, 135, 135, 59, 20, 20, 8, 8, 135] 135 rigid atoms, others: [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]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580737 none N#CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CN=C1C(F)(F)F NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 5, 15, 15, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 44, 63, 135, 135, 135, 135, 135, 1, 1, 1, 1, 2, 2, 2, 1, 7, 44, 44, 63, 63, 1] 135 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 23, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580737 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580737 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580737/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580737 Building REAL300025580738 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580738' /scratch/stefan/7787361/working/building/REAL300025580738 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580738 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580738/0 /scratch/stefan/7787361/working/building/REAL300025580738 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/233 `/scratch/stefan/7787361/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1) `REAL300025580738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580738 none CC(C)C(=O)NC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 153, 201, 153, 153, 118, 118, 118, 45, 45, 45, 15, 7, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 201, 201, 201, 201, 201, 201, 201, 153, 118, 45, 15, 15, 7, 7, 118, 118] 201 rigid atoms, others: [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: 694 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580738 none CC(C)C(=O)NC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 3, 14, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 27, 31, 118, 118, 118, 118, 118, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 3, 1, 5, 27, 27, 31, 31, 1, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 20, 21, 22, 38, 37, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580738 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580738 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580738/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580738 Building REAL300025580739 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580739' /scratch/stefan/7787361/working/building/REAL300025580739 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580739 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580739/0 /scratch/stefan/7787361/working/building/REAL300025580739 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/234 `/scratch/stefan/7787361/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC(F)F)C(F)=C1) `REAL300025580739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580739 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC(F)F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 23, 23, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 9, 21, 21, 1, 1, 1, 5, 23, 23, 23, 23, 1, 1, 21, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 19, 20, 21, 27, 28, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 29]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580739 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC(F)F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 15, 7, 1, 1, 1, 1, 1, 1, 1, 31, 86, 86, 86, 86, 185, 201, 201, 86, 86, 86, 31, 15, 15, 7, 7, 86, 86, 201, 86] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 450 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580739 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580739 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580739/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580739 Building REAL300025580740 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580740' /scratch/stefan/7787361/working/building/REAL300025580740 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580740 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580740/0 /scratch/stefan/7787361/working/building/REAL300025580740 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/235 `/scratch/stefan/7787361/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(C)C)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580740 none CCC1=NC(C(C)C)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 179, 179, 179, 179, 195, 195, 179, 179, 61, 61, 61, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 195, 195, 195, 195, 195, 195, 195, 179, 179, 61, 19, 19, 8, 8] 201 rigid atoms, others: [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: 591 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580740 none CCC1=NC(C(C)C)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 10, 10, 10, 54, 60, 179, 179, 179, 179, 179, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 1, 1, 10, 54, 54, 60, 60] 201 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 34, 35] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580740 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580740 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580740/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580740 Building REAL300025580741 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580741' /scratch/stefan/7787361/working/building/REAL300025580741 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580741 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580741/0 /scratch/stefan/7787361/working/building/REAL300025580741 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/236 `/scratch/stefan/7787361/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCN(C2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=N2)C1) `REAL300025580741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580741 none CC1CCCN(C2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 138, 138, 138, 57, 57, 57, 17, 8, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 57, 17, 17, 8, 8, 138, 138, 201, 201] 201 rigid atoms, others: [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, 40, 41, 42, 43]) total number of confs: 425 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580741 none CC1CCCN(C2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 5, 29, 33, 138, 138, 138, 138, 138, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 5, 29, 29, 33, 33, 1, 1, 7, 7] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 40, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580741 none CC1CCCN(C2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 23, 111, 120, 201, 201, 201, 201, 201, 7, 7, 7, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 23, 111, 111, 120, 120, 7, 7, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 42, 43, 23, 33, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580741 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580741 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580741/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580741 Building REAL300025580742 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580742' /scratch/stefan/7787361/working/building/REAL300025580742 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580742 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580742/0 /scratch/stefan/7787361/working/building/REAL300025580742 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/237 `/scratch/stefan/7787361/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(NC2=CC=CC=C2)SC=N1) `REAL300025580742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580742 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(NC2=CC=CC=C2)SC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 14, 33, 33, 110, 122, 201, 201, 201, 201, 201, 14, 6, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 33, 110, 110, 122, 122, 6, 1, 1, 1, 1, 1, 14] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 600 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580742 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(NC2=CC=CC=C2)SC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 22, 40, 159, 159, 159, 160, 160, 1, 1, 1, 6, 14, 14, 6, 14, 14, 1, 1, 1, 5, 21, 21, 40, 40, 6, 14, 14, 9, 14, 14, 1] 201 rigid atoms, others: [1, 34, 11, 12, 13, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580742 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(NC2=CC=CC=C2)SC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 22, 8, 1, 1, 1, 1, 1, 1, 1, 91, 160, 160, 201, 201, 201, 201, 201, 201, 160, 159, 159, 90, 22, 22, 8, 8, 201, 201, 201, 201, 201, 201, 159] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 549 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580742 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580742 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580742/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580742 Building REAL300025580743 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580743' /scratch/stefan/7787361/working/building/REAL300025580743 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580743 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580743/0 /scratch/stefan/7787361/working/building/REAL300025580743 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/238 `/scratch/stefan/7787361/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580743 none C[NH+](C)CCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 155, 143, 143, 143, 143, 59, 59, 59, 17, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 155, 155, 143, 143, 59, 17, 17, 8, 8, 143, 143] 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, 41]) total number of confs: 660 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580743 none C[NH+](C)CCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 9, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 37, 143, 143, 143, 143, 143, 1, 1, 9, 9, 9, 9, 9, 9, 5, 5, 3, 3, 1, 1, 5, 29, 29, 37, 37, 1, 1] 201 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 322 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580743 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580743 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580743/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580743 Building REAL300025580744 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580744' /scratch/stefan/7787361/working/building/REAL300025580744 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580744 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580744/0 /scratch/stefan/7787361/working/building/REAL300025580744 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/239 `/scratch/stefan/7787361/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C(NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580744 none CC1=CC=CC=C1C(NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 113, 97, 38, 97, 154, 197, 197, 200, 200, 200, 200, 38, 38, 17, 8, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 113, 113, 97, 154, 200, 200, 200, 200, 200, 200, 200, 200, 200, 38, 17, 17, 8, 8] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 777 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580744 none CC1=CC=CC=C1C(NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 16, 16, 20, 20, 20, 20, 4, 15, 15, 15, 50, 53, 113, 113, 113, 113, 113, 2, 2, 2, 1, 1, 1, 1, 4, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 15, 50, 50, 53, 53] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 352 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580744 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580744 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580744/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580744 Building REAL300025580745 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580745' /scratch/stefan/7787361/working/building/REAL300025580745 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580745 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580745/0 /scratch/stefan/7787361/working/building/REAL300025580745 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/240 `/scratch/stefan/7787361/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(Br)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL300025580745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580745 none CN1C=C(Br)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 163, 163, 93, 93, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 163, 93, 24, 24, 8, 8] 163 rigid atoms, others: [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]) total number of confs: 389 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580745 none CN1C=C(Br)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 67, 163, 163, 163, 163, 163, 1, 2, 2, 2, 1, 7, 37, 37, 67, 67] 163 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 21] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580745 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580745 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580745/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580745 Building REAL300025580746 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580746' /scratch/stefan/7787361/working/building/REAL300025580746 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580746 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580746/0 /scratch/stefan/7787361/working/building/REAL300025580746 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/241 `/scratch/stefan/7787361/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)SC(Cl)=N1) `REAL300025580746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580746 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)SC(Cl)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 14, 1, 16, 8, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [5, 1, 5, 5, 33, 59, 163, 163, 163, 163, 163, 1, 1, 1, 1, 1, 1, 1, 5, 33, 33, 59, 59] 163 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 413 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580746 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)SC(Cl)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 14, 1, 16, 8, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [96, 96, 24, 8, 1, 1, 1, 1, 1, 1, 1, 96, 163, 163, 163, 163, 163, 163, 96, 24, 24, 8, 8] 163 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580746 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580746 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580746/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580746 Building REAL300025580747 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580747' /scratch/stefan/7787361/working/building/REAL300025580747 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580747 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580747/0 /scratch/stefan/7787361/working/building/REAL300025580747 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/242 `/scratch/stefan/7787361/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C(=O)CCNC1=S)NCCC1=NC(=O)O[N-]1) `REAL300025580747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580747 none O=C(CCN1C(=O)CCNC1=S)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'S.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 14, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 130, 130, 201, 201, 201, 201, 201, 201, 201, 21, 8, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 201, 201, 201, 201, 201, 58, 21, 21, 8, 8] 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]) total number of confs: 645 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580747 none O=C(CCN1C(=O)CCNC1=S)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'S.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 14, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 95, 103, 201, 201, 201, 201, 201, 5, 5, 3, 3, 1, 1, 1, 1, 1, 22, 95, 95, 103, 103] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 29] set([0, 1, 2, 34, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 554 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580747 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580747 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580747/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580747 Building REAL300025580748 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580748' /scratch/stefan/7787361/working/building/REAL300025580748 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580748 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580748/0 /scratch/stefan/7787361/working/building/REAL300025580748 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/243 `/scratch/stefan/7787361/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(OC2CCOCC2)C(Cl)=C1) `REAL300025580748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580748 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(OC2CCOCC2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 12, 5, 5, 5, 12, 5, 5, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 50, 50, 127, 127, 201, 201, 201, 201, 201, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 20, 19, 20, 50, 127, 127, 127, 127, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 31] 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, 40]) total number of confs: 584 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580748 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(OC2CCOCC2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 12, 5, 5, 5, 12, 5, 5, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 25, 28, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 5, 20, 20, 20, 20, 20, 1, 1, 1, 5, 25, 25, 28, 28, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1] 201 rigid atoms, others: [1, 40, 11, 12, 13, 14, 15, 22, 23, 24, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580748 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(OC2CCOCC2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 12, 5, 5, 5, 12, 5, 5, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 41, 104, 104, 104, 104, 130, 201, 201, 201, 201, 201, 104, 104, 104, 41, 17, 17, 8, 8, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580748 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580748 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580748/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580748 Building REAL300025580749 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580749' /scratch/stefan/7787361/working/building/REAL300025580749 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580749 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580749/0 /scratch/stefan/7787361/working/building/REAL300025580749 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/244 `/scratch/stefan/7787361/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C2OCOC2=C1) `REAL300025580749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580749 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 29, 29, 30, 108, 116, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 8, 29, 108, 108, 116, 116, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 601 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580749 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 57, 57, 57, 19, 8, 1, 1, 1, 1, 1, 1, 1, 139, 201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 139, 139, 56, 20, 20, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 649 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580749 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580749 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580749/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580749 Building REAL300025580750 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580750' /scratch/stefan/7787361/working/building/REAL300025580750 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580750 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580750/0 /scratch/stefan/7787361/working/building/REAL300025580750 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/245 `/scratch/stefan/7787361/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=NOC3=CC=C(Cl)C=C32)CC1) `REAL300025580750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580750 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=NOC3=CC=C(Cl)C=C32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 8, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 37, 37, 102, 103, 201, 201, 201, 201, 201, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 37, 102, 102, 103, 103, 5, 5, 6, 5, 5, 1, 1, 1, 5, 5, 5, 6] 201 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 523 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580750 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=NOC3=CC=C(Cl)C=C32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 8, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 50, 51, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 6, 5, 1, 1, 12, 50, 50, 51, 51, 1, 1, 1, 1, 1, 5, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 33, 40, 41, 42, 11, 12, 13, 14, 15, 43, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580750 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=NOC3=CC=C(Cl)C=C32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 8, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 42, 120, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 42, 17, 17, 8, 8, 120, 120, 120, 120, 120, 201, 201, 201, 120, 120, 120, 120] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 508 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580750 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580750 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580750/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580750 Building REAL300025580751 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580751' /scratch/stefan/7787361/working/building/REAL300025580751 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580751 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580751/0 /scratch/stefan/7787361/working/building/REAL300025580751 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/246 `/scratch/stefan/7787361/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1[N+](=O)[O-]) `REAL300025580751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580751 none CC1=CC(Cl)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 167, 87, 87, 87, 23, 8, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 167, 167, 167, 167, 87, 23, 23, 8, 8, 167] 167 rigid atoms, others: [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]) total number of confs: 396 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580751 none CC1=CC(Cl)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 63, 167, 167, 167, 167, 167, 1, 1, 1, 2, 2, 2, 2, 2, 1, 7, 39, 39, 63, 63, 1] 167 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 429 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580751 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580751 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580751/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580751 Building REAL300025580752 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580752' /scratch/stefan/7787361/working/building/REAL300025580752 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580752 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580752/0 /scratch/stefan/7787361/working/building/REAL300025580752 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/247 `/scratch/stefan/7787361/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C(=O)NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21) `REAL300025580752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580752 none CC1(C)C(=O)NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 115, 115, 115, 115, 53, 53, 53, 22, 8, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 52, 22, 22, 8, 8, 115, 115] 115 rigid atoms, others: [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: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580752 none CC1(C)C(=O)NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 56, 115, 115, 115, 115, 115, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 7, 37, 37, 56, 56, 1, 1] 115 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 36, 29, 30, 37] set([32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580752 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580752 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580752/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580752 Building REAL300025580753 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580753' /scratch/stefan/7787361/working/building/REAL300025580753 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580753 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580753/0 /scratch/stefan/7787361/working/building/REAL300025580753 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/248 `/scratch/stefan/7787361/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CCC1(O)CC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025580753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580753 none CC(C)(C)CCC1(O)CC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 132, 132, 132, 132, 54, 54, 54, 19, 8, 1, 1, 1, 1, 1, 1, 1, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 396, 132, 132, 132, 54, 19, 19, 8, 8, 132, 132] 603 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, 41, 42, 43, 44, 45]) total number of confs: 1234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580753 none CC(C)(C)CCC1(O)CC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 54, 59, 132, 132, 132, 132, 132, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 11, 54, 54, 59, 59, 1, 1] 603 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580753 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580753 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580753/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580753 Building REAL300025580754 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580754' /scratch/stefan/7787361/working/building/REAL300025580754 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580754 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580754/0 /scratch/stefan/7787361/working/building/REAL300025580754 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/249 `/scratch/stefan/7787361/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2=CC=CC=C2)N=CO1) `REAL300025580754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580754 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2=CC=CC=C2)N=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 6, 29, 29, 97, 113, 201, 201, 201, 201, 201, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 29, 97, 97, 113, 113, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 32]) total number of confs: 595 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580754 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2=CC=CC=C2)N=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 64, 81, 177, 177, 177, 177, 177, 1, 1, 1, 6, 6, 3, 6, 6, 1, 1, 1, 12, 64, 64, 81, 81, 6, 6, 3, 6, 6, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 481 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580754 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2=CC=CC=C2)N=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 8, 1, 1, 1, 1, 1, 1, 1, 66, 177, 177, 201, 201, 200, 201, 201, 177, 177, 177, 65, 22, 22, 8, 8, 201, 201, 200, 201, 201, 177] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 426 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580754 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580754 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580754/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580754 Building REAL300025580755 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580755' /scratch/stefan/7787361/working/building/REAL300025580755 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580755 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580755/0 /scratch/stefan/7787361/working/building/REAL300025580755 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/250 `/scratch/stefan/7787361/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1) `REAL300025580755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580755 none CCOC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 197, 111, 197, 111, 111, 111, 92, 92, 92, 23, 8, 1, 1, 1, 1, 1, 1, 1, 111, 111, 201, 201, 201, 201, 201, 111, 111, 92, 23, 23, 8, 8, 111] 201 rigid atoms, others: [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: 622 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580755 none CCOC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 4, 18, 27, 111, 111, 111, 111, 111, 1, 1, 30, 30, 30, 29, 29, 1, 1, 4, 18, 18, 27, 27, 1] 201 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 20, 21, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580755 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580755 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580755/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580755 Building REAL300025580756 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580756' /scratch/stefan/7787361/working/building/REAL300025580756 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580756 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580756/0 /scratch/stefan/7787361/working/building/REAL300025580756 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/251 `/scratch/stefan/7787361/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC(=O)C1=CC=CC([N+](=O)[O-])=C1)NCCC1=NC(=O)O[N-]1) `REAL300025580756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580756 none O=C(CCC(=O)C1=CC=CC([N+](=O)[O-])=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 92, 96, 146, 146, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 92, 92, 96, 96, 201, 201, 201, 201, 37, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 673 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580756 none O=C(CCC(=O)C1=CC=CC([N+](=O)[O-])=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 61, 61, 100, 102, 201, 201, 201, 201, 201, 30, 30, 24, 24, 1, 1, 1, 1, 61, 100, 100, 102, 102] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 583 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580756 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580756 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580756/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580756 Building REAL300025580757 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580757' /scratch/stefan/7787361/working/building/REAL300025580757 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580757 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580757/0 /scratch/stefan/7787361/working/building/REAL300025580757 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/252 `/scratch/stefan/7787361/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H]2[C@H](C(=O)NCCC3=NC(=O)O[N-]3)[C@H]2C1) `REAL300025580757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580757 none CC(C)(C)OC(=O)N1C[C@H]2[C@H](C(=O)NCCC3=NC(=O)O[N-]3)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 159, 119, 159, 119, 119, 119, 119, 32, 119, 32, 32, 17, 9, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 32, 17, 17, 9, 9, 119, 119] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 589 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580757 none CC(C)(C)OC(=O)N1C[C@H]2[C@H](C(=O)NCCC3=NC(=O)O[N-]3)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 42, 42, 119, 119, 119, 119, 119, 1, 1, 1, 6, 6, 6, 5, 5, 5, 6, 6, 6, 1, 1, 13, 42, 42, 42, 42, 1, 1] 201 rigid atoms, others: [43, 36, 5, 7, 8, 9, 10, 11, 12, 13, 44, 24, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580757 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580757 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580757/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580757 Building REAL300025580758 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580758' /scratch/stefan/7787361/working/building/REAL300025580758 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580758 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580758/0 /scratch/stefan/7787361/working/building/REAL300025580758 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/253 `/scratch/stefan/7787361/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1OCCC2=C1C=CS2) `REAL300025580758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580758 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1OCCC2=C1C=CS2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 11, 11, 11, 46, 62, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 46, 46, 62, 62, 1, 1, 1, 1, 1, 1, 1] 131 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 359 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580758 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1OCCC2=C1C=CS2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [119, 82, 82, 82, 23, 8, 1, 1, 1, 1, 1, 1, 1, 119, 131, 131, 131, 131, 131, 131, 131, 131, 119, 119, 119, 119, 82, 24, 24, 8, 8, 131, 131, 131, 131, 131, 131, 131] 131 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 516 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580758 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580758 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580758/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580758 Building REAL300025580759 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580759' /scratch/stefan/7787361/working/building/REAL300025580759 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580759 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580759/0 /scratch/stefan/7787361/working/building/REAL300025580759 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/254 `/scratch/stefan/7787361/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC(OCC2CCCO2)CC1) `REAL300025580759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580759 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC(OCC2CCCO2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 42, 42, 111, 111, 201, 201, 201, 201, 201, 24, 24, 24, 17, 8, 1, 1, 1, 1, 1, 1, 24, 24, 42, 111, 111, 111, 111, 24, 24, 24, 24, 24, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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, 44, 45, 46, 47]) total number of confs: 568 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580759 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC(OCC2CCCO2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 24, 26, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 6, 11, 24, 24, 24, 24, 1, 1, 4, 24, 24, 26, 26, 1, 1, 1, 1, 1, 1, 11, 11, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 44, 11, 12, 13, 14, 15, 46, 22, 23, 45, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580759 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC(OCC2CCCO2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 17, 8, 1, 1, 1, 1, 1, 1, 1, 40, 82, 82, 82, 82, 150, 173, 201, 201, 201, 201, 82, 82, 40, 17, 17, 8, 8, 82, 82, 82, 82, 82, 82, 173, 173, 201, 201, 201, 201, 201, 201, 201, 82, 82, 82, 82] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 648 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580759 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580759 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580759/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580759 Building REAL300025580760 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580760' /scratch/stefan/7787361/working/building/REAL300025580760 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580760 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580760/0 /scratch/stefan/7787361/working/building/REAL300025580760 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/255 `/scratch/stefan/7787361/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=C(F)C=C1Cl) `REAL300025580760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580760 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 15, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 43, 63, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 43, 43, 63, 63, 1, 1] 153 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 395 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580760 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 15, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 22, 8, 1, 1, 1, 1, 1, 1, 1, 82, 153, 153, 153, 153, 121, 153, 153, 153, 82, 22, 22, 8, 8, 153, 153] 153 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 393 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580760 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580760 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580760/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580760 Building REAL300025580761 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580761' /scratch/stefan/7787361/working/building/REAL300025580761 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580761 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580761/0 /scratch/stefan/7787361/working/building/REAL300025580761 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/256 `/scratch/stefan/7787361/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580761 none C#CCCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 102, 102, 32, 32, 72, 72, 32, 32, 32, 15, 7, 1, 1, 1, 1, 1, 1, 1, 72, 72, 201, 201, 201, 102, 102, 72, 72, 32, 15, 15, 7, 7, 72, 72] 201 rigid atoms, others: [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]) total number of confs: 822 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580761 none C#CCCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 23, 72, 72, 72, 72, 72, 1, 1, 14, 13, 13, 5, 5, 1, 1, 5, 23, 23, 23, 23, 1, 1] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 20, 21, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580761 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580761 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580761/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580761 Building REAL300025580762 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580762' /scratch/stefan/7787361/working/building/REAL300025580762 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580762 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580762/0 /scratch/stefan/7787361/working/building/REAL300025580762 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/257 `/scratch/stefan/7787361/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(Br)C=CC=C2C=N1) `REAL300025580762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580762 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(Br)C=CC=C2C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 54, 68, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 54, 54, 68, 68, 1, 1, 1, 1, 1] 145 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580762 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(Br)C=CC=C2C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [84, 84, 20, 8, 1, 1, 1, 1, 1, 1, 1, 84, 145, 145, 145, 145, 145, 145, 145, 145, 144, 144, 83, 20, 20, 8, 8, 145, 145, 145, 144, 144] 145 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580762 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580762 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580762/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580762 Building REAL300025580763 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580763' /scratch/stefan/7787361/working/building/REAL300025580763 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580763 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580763/0 /scratch/stefan/7787361/working/building/REAL300025580763 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/258 `/scratch/stefan/7787361/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1I) `REAL300025580763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580763 none CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1I NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 18, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 171, 89, 89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 171, 171, 89, 24, 24, 8, 8] 171 rigid atoms, others: [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]) total number of confs: 393 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580763 none CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1I NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 18, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 43, 69, 171, 171, 171, 171, 171, 1, 1, 2, 2, 2, 1, 7, 43, 43, 69, 69] 171 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 21] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580763 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580763 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580763/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580763 Building REAL300025580764 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580764' /scratch/stefan/7787361/working/building/REAL300025580764 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580764 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580764/0 /scratch/stefan/7787361/working/building/REAL300025580764 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/259 `/scratch/stefan/7787361/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1=CC=C(Cl)C(F)=C1)NCCC1=NC(=O)O[N-]1) `REAL300025580764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580764 none O=C(COC1=CC=C(Cl)C(F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 16, 1, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 94, 137, 201, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 101, 101, 201, 201, 201, 34, 8, 8, 8, 8] 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]) total number of confs: 563 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580764 none O=C(COC1=CC=C(Cl)C(F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 16, 1, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 125, 125, 201, 201, 201, 201, 201, 19, 19, 1, 1, 1, 65, 125, 125, 125, 125] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580764 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580764 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580764/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580764 Building REAL300025580765 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580765' /scratch/stefan/7787361/working/building/REAL300025580765 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580765 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580765/0 /scratch/stefan/7787361/working/building/REAL300025580765 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/260 `/scratch/stefan/7787361/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(N2C=C(C(=O)NCCC3=NC(=O)O[N-]3)N=N2)=C1) `REAL300025580765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580765 none COC1=CC=CC(N2C=C(C(=O)NCCC3=NC(=O)O[N-]3)N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 135, 135, 135, 81, 81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 134, 134, 201, 201, 201, 201, 201, 201, 201, 135, 80, 24, 24, 8, 8, 201] 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]) total number of confs: 473 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580765 none COC1=CC=CC(N2C=C(C(=O)NCCC3=NC(=O)O[N-]3)N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 5, 4, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 24, 37, 134, 134, 134, 134, 134, 1, 1, 5, 7, 7, 7, 4, 5, 5, 1, 6, 24, 24, 37, 37, 5] 201 rigid atoms, others: [6, 7, 8, 9, 10, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580765 none COC1=CC=CC(N2C=C(C(=O)NCCC3=NC(=O)O[N-]3)N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 46, 66, 201, 201, 201, 201, 201, 5, 5, 1, 3, 3, 3, 1, 1, 1, 5, 13, 46, 46, 66, 66, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 23, 36, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 445 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580765 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580765 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580765/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580765 Building REAL300025580766 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580766' /scratch/stefan/7787361/working/building/REAL300025580766 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580766 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580766/0 /scratch/stefan/7787361/working/building/REAL300025580766 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/261 `/scratch/stefan/7787361/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCCS(=O)(=O)C1)NCCC1=NC(=O)O[N-]1) `REAL300025580766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580766 none O=C(CC1CCCS(=O)(=O)C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 158, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 56, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 750 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580766 none O=C(CC1CCCS(=O)(=O)C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 99, 105, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 99, 99, 105, 105] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 34, 35, 33, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31]) total number of confs: 566 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580766 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580766 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580766/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580766 Building REAL300025580767 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580767' /scratch/stefan/7787361/working/building/REAL300025580767 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580767 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580767/0 /scratch/stefan/7787361/working/building/REAL300025580767 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/262 `/scratch/stefan/7787361/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)N1) `REAL300025580767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580767 none COCCOCCC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 189, 173, 155, 155, 85, 85, 85, 85, 50, 50, 50, 17, 8, 1, 1, 1, 1, 1, 1, 1, 85, 201, 201, 201, 201, 201, 189, 189, 155, 155, 155, 155, 85, 50, 17, 17, 8, 8, 85] 201 rigid atoms, others: [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: 765 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580767 none COCCOCCC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 43, 23, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 20, 21, 85, 85, 85, 85, 85, 1, 52, 52, 52, 43, 43, 23, 23, 5, 5, 5, 5, 1, 5, 20, 20, 21, 21, 1] 201 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 40, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580767 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580767 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580767/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580767 Building REAL300025580768 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580768' /scratch/stefan/7787361/working/building/REAL300025580768 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580768 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580768/0 /scratch/stefan/7787361/working/building/REAL300025580768 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/263 `/scratch/stefan/7787361/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C=C(Br)C=N1)NCCC1=NC(=O)O[N-]1) `REAL300025580768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580768 none O=C(CCN1C=C(Br)C=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 17, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 163, 179, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 163, 163, 179, 179, 201, 201, 57, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 756 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580768 none O=C(CCN1C=C(Br)C=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 17, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 8, 1, 1, 1, 1, 1, 1, 1, 48, 48, 121, 127, 201, 201, 201, 201, 201, 12, 12, 8, 8, 1, 1, 48, 123, 123, 127, 126] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 634 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580768 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580768 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580768/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580768 Building REAL300025580769 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580769' /scratch/stefan/7787361/working/building/REAL300025580769 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025580769 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580769/0 /scratch/stefan/7787361/working/building/REAL300025580769 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/264 `/scratch/stefan/7787361/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=C(C1)C1=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C1N2) `REAL300025580769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580769 none CN1CCC2=C(C1)C1=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C1N2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 139, 139, 139, 139, 139, 64, 64, 64, 23, 8, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 63, 23, 23, 8, 8, 139, 139, 139] 139 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, 41, 42]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580769 none CN1CCC2=C(C1)C1=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C1N2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 38, 56, 139, 139, 139, 139, 139, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 38, 38, 56, 56, 1, 1, 1] 139 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42] set([35, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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/7787361/working/building/REAL300025580769 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025580769/1 /scratch/stefan/7787361/working/building/REAL300025580769 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/265 `/scratch/stefan/7787361/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCC2=C(C1)C1=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C1N2) `REAL300025580769.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025580769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580769 none C[N@@H+]1CCC2=C(C1)C1=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C1N2 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 24, 24, 24, 17, 8, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 24, 17, 17, 8, 8, 30, 30, 30] 30 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580769 none C[N@@H+]1CCC2=C(C1)C1=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C1N2 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 12, 15, 30, 30, 30, 30, 30, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 12, 12, 15, 15, 1, 1, 1] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43] set([36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580769 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `2' /scratch/stefan/7787361/working/building/REAL300025580769/2 /scratch/stefan/7787361/working/building/REAL300025580769 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 2 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/266 `/scratch/stefan/7787361/working/3D/266' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCC2=C(C1)C1=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C1N2) `REAL300025580769.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025580769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580769/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580769 none C[N@H+]1CCC2=C(C1)C1=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C1N2 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 23, 16, 8, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 16, 16, 8, 8, 30, 30, 30] 30 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580769 none C[N@H+]1CCC2=C(C1)C1=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C1N2 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 12, 15, 30, 30, 30, 30, 30, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 12, 12, 15, 15, 1, 1, 1] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43] set([36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580769 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580769 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 2: /scratch/stefan/7787361/working/building/REAL300025580769/2.* 1: /scratch/stefan/7787361/working/building/REAL300025580769/1.* 0: /scratch/stefan/7787361/working/building/REAL300025580769/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580769 Building REAL300025580770 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580770' /scratch/stefan/7787361/working/building/REAL300025580770 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580770 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580770/0 /scratch/stefan/7787361/working/building/REAL300025580770 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/267 `/scratch/stefan/7787361/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(OC1=CC=C(Cl)C=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580770 none CC(C)C(OC1=CC=C(Cl)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 102, 127, 35, 102, 179, 187, 187, 184, 184, 187, 187, 35, 35, 14, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 127, 127, 102, 187, 187, 187, 187, 35, 14, 14, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 675 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580770 none CC(C)C(OC1=CC=C(Cl)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 36, 36, 36, 98, 102, 187, 187, 187, 187, 187, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 36, 98, 98, 102, 102] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 12, 13, 14, 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: 589 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580770 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580770 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580770/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580770 Building REAL300025580771 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580771' /scratch/stefan/7787361/working/building/REAL300025580771 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580771 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580771/0 /scratch/stefan/7787361/working/building/REAL300025580771 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/268 `/scratch/stefan/7787361/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N2C=C(Cl)C=CC2=N1) `REAL300025580771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580771 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N2C=C(Cl)C=CC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 155, 155, 47, 47, 47, 17, 8, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 155, 155, 155, 201, 201, 201, 201, 201, 47, 17, 17, 8, 8, 155, 155, 155] 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, 34, 35]) total number of confs: 582 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580771 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N2C=C(Cl)C=CC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 11, 11, 11, 49, 53, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 49, 49, 53, 53, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 35, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 361 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580771 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580771 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580771/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580771 Building REAL300025580772 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580772' /scratch/stefan/7787361/working/building/REAL300025580772 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580772 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580772/0 /scratch/stefan/7787361/working/building/REAL300025580772 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/269 `/scratch/stefan/7787361/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=C(C(F)(F)F)C=C2)O1) `REAL300025580772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580772 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=C(C(F)(F)F)C=C2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 39, 39, 105, 119, 201, 201, 201, 201, 201, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 39, 105, 105, 121, 121, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580772 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=C(C(F)(F)F)C=C2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 38, 54, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 7, 7, 1, 1, 6, 6, 7, 7, 7, 1, 8, 37, 37, 54, 54, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 25, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 387 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580772 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=C(C(F)(F)F)C=C2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 77, 151, 151, 151, 151, 201, 201, 151, 151, 201, 201, 201, 201, 201, 151, 76, 23, 23, 8, 8, 151, 151, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 913 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580772 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580772 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580772/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580772 Building REAL300025580773 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580773' /scratch/stefan/7787361/working/building/REAL300025580773 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580773 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580773/0 /scratch/stefan/7787361/working/building/REAL300025580773 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/270 `/scratch/stefan/7787361/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC2=CC=C(Br)C=C21) `REAL300025580773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580773 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC2=CC=C(Br)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 89, 89, 89, 20, 8, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 157, 157, 157, 157, 157, 157, 157, 88, 21, 21, 8, 8, 157, 157, 157] 157 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 382 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580773 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC2=CC=C(Br)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 9, 9, 9, 47, 73, 157, 157, 157, 157, 157, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 47, 47, 73, 73, 1, 1, 1] 157 rigid atoms, others: [0, 1, 2, 3, 32, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 456 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580773 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580773 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580773/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580773 Building REAL300025580774 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580774' /scratch/stefan/7787361/working/building/REAL300025580774 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580774 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580774/0 /scratch/stefan/7787361/working/building/REAL300025580774 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/271 `/scratch/stefan/7787361/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1[N+](=O)[O-]) `REAL300025580774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580774 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 3, 7, 7, 7, 44, 73, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 7, 44, 44, 73, 73, 1, 1, 1, 1] 144 rigid atoms, others: [1, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20] set([0, 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]) total number of confs: 438 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580774 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [142, 81, 142, 81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 142, 144, 144, 144, 144, 144, 144, 144, 144, 142, 142, 142, 142, 142, 142, 81, 25, 25, 8, 8, 144, 144, 144, 144] 144 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 539 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580774 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580774 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580774/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580774 Building REAL300025580775 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580775' /scratch/stefan/7787361/working/building/REAL300025580775 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580775 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580775/0 /scratch/stefan/7787361/working/building/REAL300025580775 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/272 `/scratch/stefan/7787361/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(F)C=CC(F)=C2N=C1) `REAL300025580775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580775 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(F)C=CC(F)=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [7, 1, 7, 7, 43, 65, 150, 150, 150, 150, 150, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 43, 43, 65, 65, 1, 1, 1, 1] 150 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27]) total number of confs: 393 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580775 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(F)C=CC(F)=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [67, 67, 20, 8, 1, 1, 1, 1, 1, 1, 1, 67, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 66, 20, 20, 8, 8, 150, 150, 150, 150] 150 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580775 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580775 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580775/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580775 Building REAL300025580776 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580776' /scratch/stefan/7787361/working/building/REAL300025580776 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580776 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580776/0 /scratch/stefan/7787361/working/building/REAL300025580776 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/273 `/scratch/stefan/7787361/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC=C2C(Br)=C1) `REAL300025580776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580776 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC=C2C(Br)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 41, 59, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 59, 59, 1, 1, 1, 1, 1, 1] 135 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580776 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC=C2C(Br)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 20, 8, 1, 1, 1, 1, 1, 1, 1, 55, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 54, 20, 21, 8, 8, 135, 135, 135, 135, 135, 135] 135 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580776 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580776 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580776/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580776 Building REAL300025580777 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580777' /scratch/stefan/7787361/working/building/REAL300025580777 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580777 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580777/0 /scratch/stefan/7787361/working/building/REAL300025580777 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/274 `/scratch/stefan/7787361/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCN(C2=CC=CC=C2)C1=O) `REAL300025580777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580777 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCN(C2=CC=CC=C2)C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 4, 28, 28, 93, 110, 201, 201, 201, 201, 201, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 28, 93, 93, 110, 110, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1] 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]) total number of confs: 568 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580777 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCN(C2=CC=CC=C2)C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 57, 76, 200, 200, 200, 200, 200, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 13, 57, 57, 76, 76, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4] 201 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40]) total number of confs: 488 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580777 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCN(C2=CC=CC=C2)C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 24, 8, 1, 1, 1, 1, 1, 1, 1, 88, 200, 200, 200, 200, 200, 201, 201, 200, 201, 201, 200, 200, 87, 24, 24, 8, 8, 200, 200, 200, 200, 200, 200, 200, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 603 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580777 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580777 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580777/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580777 Building REAL300025580778 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580778' /scratch/stefan/7787361/working/building/REAL300025580778 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580778 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580778/0 /scratch/stefan/7787361/working/building/REAL300025580778 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/275 `/scratch/stefan/7787361/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(CCC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580778 none NC(=O)C1=CC=C(CCC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 123, 201, 123, 201, 201, 123, 113, 46, 46, 46, 18, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 123, 123, 113, 113, 46, 18, 18, 7, 7, 201, 201] 201 rigid atoms, others: [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: 1195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580778 none NC(=O)C1=CC=C(CCC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 2, 6, 25, 25, 25, 107, 108, 201, 201, 201, 201, 201, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 25, 107, 107, 108, 108, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 20, 21, 24, 25, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580778 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580778 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580778/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580778 Building REAL300025580779 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580779' /scratch/stefan/7787361/working/building/REAL300025580779 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580779 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580779/0 /scratch/stefan/7787361/working/building/REAL300025580779 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/276 `/scratch/stefan/7787361/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)N(C(=O)OC(C)(C)C)C1CC1) `REAL300025580779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580779 none CC(C(=O)NCCC1=NC(=O)O[N-]1)N(C(=O)OC(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 6, 16, 16, 16, 57, 67, 147, 147, 147, 147, 147, 1, 4, 7, 7, 12, 12, 12, 12, 1, 1, 1, 6, 6, 6, 6, 16, 57, 57, 67, 67, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 13, 46, 45, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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]) total number of confs: 417 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580779 none CC(C(=O)NCCC1=NC(=O)O[N-]1)N(C(=O)OC(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 61, 61, 22, 8, 1, 1, 1, 1, 1, 1, 1, 105, 124, 156, 156, 170, 170, 170, 170, 124, 147, 147, 105, 105, 105, 105, 61, 23, 23, 8, 8, 170, 170, 170, 170, 170, 170, 170, 170, 170, 147, 147, 147, 147, 147] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 732 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580779 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580779 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580779/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580779 Building REAL300025580780 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580780' /scratch/stefan/7787361/working/building/REAL300025580780 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580780 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580780/0 /scratch/stefan/7787361/working/building/REAL300025580780 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/277 `/scratch/stefan/7787361/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(I)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580780 none CN1N=CC(I)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'I', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 18, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [187, 187, 187, 187, 187, 187, 120, 120, 120, 24, 8, 1, 1, 1, 1, 1, 1, 1, 187, 187, 187, 187, 120, 24, 24, 8, 8] 187 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]) total number of confs: 450 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580780 none CN1N=CC(I)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'I', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 18, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 66, 187, 187, 187, 187, 187, 2, 2, 2, 1, 7, 39, 39, 66, 66] 187 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580780 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580780 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580780/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580780 Building REAL300025580781 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580781' /scratch/stefan/7787361/working/building/REAL300025580781 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580781 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580781/0 /scratch/stefan/7787361/working/building/REAL300025580781 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/278 `/scratch/stefan/7787361/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC2=CC=C(C#N)C=C12) `REAL300025580781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580781 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC2=CC=C(C#N)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 90, 90, 90, 20, 8, 1, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 89, 20, 20, 8, 8, 156, 156, 156] 156 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580781 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC2=CC=C(C#N)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 47, 72, 156, 156, 156, 156, 156, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 47, 47, 72, 72, 1, 1, 1] 156 rigid atoms, others: [0, 1, 2, 3, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 450 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580781 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580781 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580781/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580781 Building REAL300025580782 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580782' /scratch/stefan/7787361/working/building/REAL300025580782 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580782 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580782/0 /scratch/stefan/7787361/working/building/REAL300025580782 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/279 `/scratch/stefan/7787361/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC1CCC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580782 none CC(C)(C)OC(=O)N1CCCC1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 171, 133, 171, 133, 133, 133, 133, 112, 93, 38, 38, 38, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 133, 133, 133, 133, 133, 133, 112, 112, 93, 93, 37, 8, 8, 8, 8] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580782 none CC(C)(C)OC(=O)N1CCCC1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 9, 11, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 6, 23, 23, 23, 57, 57, 133, 133, 133, 133, 133, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 23, 57, 57, 57, 57] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580782 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580782 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580782/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580782 Building REAL300025580783 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580783' /scratch/stefan/7787361/working/building/REAL300025580783 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580783 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580783/0 /scratch/stefan/7787361/working/building/REAL300025580783 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/280 `/scratch/stefan/7787361/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C(Br)=CN=C2S1) `REAL300025580783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580783 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C(Br)=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Br', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 17, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [12, 1, 12, 13, 67, 101, 198, 198, 198, 198, 198, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 67, 67, 101, 101, 1, 1] 198 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 588 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580783 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C(Br)=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Br', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 17, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [96, 96, 20, 8, 1, 1, 1, 1, 1, 1, 1, 96, 198, 198, 198, 198, 198, 198, 198, 198, 96, 20, 20, 8, 8, 198, 198] 198 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580783 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580783 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580783/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580783 Building REAL300025580784 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580784' /scratch/stefan/7787361/working/building/REAL300025580784 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580784 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580784/0 /scratch/stefan/7787361/working/building/REAL300025580784 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/281 `/scratch/stefan/7787361/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580784 none COCCOCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 184, 146, 95, 31, 19, 45, 45, 19, 19, 19, 9, 7, 1, 1, 1, 1, 1, 1, 1, 45, 45, 201, 201, 201, 201, 201, 184, 184, 95, 95, 45, 45, 19, 9, 9, 7, 7, 45, 45] 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: 852 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580784 none COCCOCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 31, 29, 17, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 21, 45, 45, 45, 45, 45, 1, 1, 41, 41, 41, 31, 31, 29, 29, 5, 5, 1, 1, 5, 21, 21, 21, 21, 1, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580784 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580784 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580784/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580784 Building REAL300025580785 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580785' /scratch/stefan/7787361/working/building/REAL300025580785 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580785 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580785/0 /scratch/stefan/7787361/working/building/REAL300025580785 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/282 `/scratch/stefan/7787361/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C(=O)CCCC2=C1) `REAL300025580785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580785 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C(=O)CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 7, 35, 54, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 35, 35, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1, 1] 113 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580785 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C(=O)CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [55, 55, 23, 8, 1, 1, 1, 1, 1, 1, 1, 55, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 54, 23, 23, 8, 8, 113, 113, 113, 113, 113, 113, 113, 113, 113] 113 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580785 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580785 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580785/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580785 Building REAL300025580786 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580786' /scratch/stefan/7787361/working/building/REAL300025580786 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580786 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580786/0 /scratch/stefan/7787361/working/building/REAL300025580786 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/283 `/scratch/stefan/7787361/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1Br) `REAL300025580786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580786 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 17, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [7, 1, 7, 7, 45, 67, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 1, 1, 1, 7, 45, 45, 67, 67, 1, 1, 1] 137 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 383 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580786 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 17, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [89, 89, 22, 8, 1, 1, 1, 1, 1, 1, 1, 89, 137, 137, 137, 137, 137, 137, 137, 89, 22, 22, 8, 8, 137, 137, 137] 137 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580786 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580786 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580786/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580786 Building REAL300025580787 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580787' /scratch/stefan/7787361/working/building/REAL300025580787 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580787 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580787/0 /scratch/stefan/7787361/working/building/REAL300025580787 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/284 `/scratch/stefan/7787361/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC=C1F) `REAL300025580787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580787 none CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 17, 10, 17, 4, 1, 4, 15, 15, 15, 48, 52, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 4, 15, 48, 48, 52, 52, 1, 1, 1] 201 rigid atoms, others: [8, 44, 45, 46, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 354 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580787 none CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 186, 149, 186, 113, 39, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 113, 131, 131, 131, 113, 131, 131, 131, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 113, 38, 8, 8, 8, 8, 131, 113, 131] 201 rigid atoms, others: [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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 805 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580787 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580787 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580787/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580787 Building REAL300025580788 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580788' /scratch/stefan/7787361/working/building/REAL300025580788 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580788 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580788/0 /scratch/stefan/7787361/working/building/REAL300025580788 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/285 `/scratch/stefan/7787361/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1C1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025580788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580788 none CC1=NOC(C)=C1C1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 92, 92, 92, 92, 92, 40, 40, 40, 15, 7, 1, 1, 1, 1, 1, 1, 1, 92, 201, 201, 201, 201, 201, 201, 92, 92, 92, 40, 15, 15, 7, 7] 201 rigid atoms, others: [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: 387 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580788 none CC1=NOC(C)=C1C1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 32, 32, 92, 92, 92, 92, 92, 1, 10, 10, 10, 10, 10, 10, 2, 2, 2, 7, 32, 32, 32, 32] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 23] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580788 none CC1=NOC(C)=C1C1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 45, 45, 45, 114, 114, 201, 201, 201, 201, 201, 10, 2, 2, 2, 2, 2, 2, 10, 10, 10, 45, 114, 114, 114, 114] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 568 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580788 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580788 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580788/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580788 Building REAL300025580789 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580789' /scratch/stefan/7787361/working/building/REAL300025580789 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025580789 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580789/0 /scratch/stefan/7787361/working/building/REAL300025580789 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/286 `/scratch/stefan/7787361/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=NC=C2)N=C1) `REAL300025580789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580789 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=NC=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 12, 12, 50, 74, 134, 134, 134, 134, 134, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 74, 74, 4, 1, 1, 1, 1, 4] 134 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 32]) total number of confs: 401 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580789 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=NC=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 31, 53, 134, 134, 134, 134, 134, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 5, 31, 31, 53, 53, 1, 4, 4, 4, 4, 1] 134 rigid atoms, others: [32, 1, 11, 12, 13, 14, 20, 21, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580789 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=NC=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 21, 8, 1, 1, 1, 1, 1, 1, 1, 68, 134, 134, 134, 134, 134, 134, 134, 134, 134, 134, 67, 21, 21, 8, 8, 134, 134, 134, 134, 134, 134] 134 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580789 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025580789/1 /scratch/stefan/7787361/working/building/REAL300025580789 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/287 `/scratch/stefan/7787361/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=[NH+]C=C2)N=C1) `REAL300025580789.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025580789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580789 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=[NH+]C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 8, 6, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 4, 7, 7, 27, 33, 57, 57, 57, 57, 57, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 27, 27, 33, 33, 4, 1, 1, 1, 1, 4] 57 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 171 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580789 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=[NH+]C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 8, 6, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 21, 25, 57, 57, 57, 57, 57, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 1, 5, 21, 21, 25, 25, 1, 4, 4, 4, 4, 1] 57 rigid atoms, others: [1, 33, 11, 12, 13, 14, 21, 22, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580789 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=[NH+]C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 8, 6, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 17, 8, 1, 1, 1, 1, 1, 1, 1, 45, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 45, 17, 17, 8, 8, 57, 57, 57, 57, 57, 57] 57 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580789 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580789 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025580789/1.* 0: /scratch/stefan/7787361/working/building/REAL300025580789/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580789 Building REAL300025580790 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580790' /scratch/stefan/7787361/working/building/REAL300025580790 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580790 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580790/0 /scratch/stefan/7787361/working/building/REAL300025580790 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/288 `/scratch/stefan/7787361/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2SN=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1) `REAL300025580790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580790 none CC1=CC=C2SN=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 200, 200, 111, 111, 111, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 110, 24, 24, 8, 8, 201] 201 rigid atoms, others: [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: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580790 none CC1=CC=C2SN=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 66, 93, 200, 200, 200, 201, 201, 1, 1, 2, 2, 2, 1, 1, 11, 65, 65, 94, 94, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 24, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 559 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580790 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580790 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580790/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580790 Building REAL300025580791 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580791' /scratch/stefan/7787361/working/building/REAL300025580791 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580791 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580791/0 /scratch/stefan/7787361/working/building/REAL300025580791 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/289 `/scratch/stefan/7787361/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(Br)=C1) `REAL300025580791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580791 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 28, 28, 28, 101, 104, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 101, 101, 104, 104, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 557 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580791 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 51, 51, 51, 19, 8, 1, 1, 1, 1, 1, 1, 1, 121, 201, 201, 201, 201, 201, 201, 121, 121, 121, 121, 51, 19, 19, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 634 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580791 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580791 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580791/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580791 Building REAL300025580792 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580792' /scratch/stefan/7787361/working/building/REAL300025580792 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580792 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580792/0 /scratch/stefan/7787361/working/building/REAL300025580792 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/290 `/scratch/stefan/7787361/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C(Br)=C1) `REAL300025580792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580792 none CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 12, 55, 55, 55, 122, 122, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 12, 12, 55, 122, 122, 122, 122, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 610 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580792 none CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 110, 40, 40, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 134, 201, 201, 201, 201, 201, 201, 201, 134, 134, 134, 134, 114, 114, 39, 8, 8, 8, 8, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580792 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580792 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580792/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580792 Building REAL300025580793 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580793' /scratch/stefan/7787361/working/building/REAL300025580793 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580793 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580793/0 /scratch/stefan/7787361/working/building/REAL300025580793 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/291 `/scratch/stefan/7787361/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=NC2=CC=CC=C2N=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580793 none CC(CC1=NC2=CC=CC=C2N=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 46, 113, 165, 201, 201, 201, 201, 201, 201, 201, 201, 201, 46, 46, 16, 8, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 165, 165, 201, 201, 201, 201, 201, 46, 16, 16, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 793 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580793 none CC(CC1=NC2=CC=CC=C2N=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 44, 44, 44, 115, 118, 201, 201, 201, 201, 201, 15, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 44, 115, 115, 118, 118] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 30, 31] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39]) total number of confs: 620 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580793 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580793 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580793/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580793 Building REAL300025580794 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580794' /scratch/stefan/7787361/working/building/REAL300025580794 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580794 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580794/0 /scratch/stefan/7787361/working/building/REAL300025580794 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/292 `/scratch/stefan/7787361/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C12CCC(C(=O)NCCC3=NC(=O)O[N-]3)(CC1)CC2) `REAL300025580794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580794 none COC(=O)C12CCC(C(=O)NCCC3=NC(=O)O[N-]3)(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 73, 165, 73, 156, 156, 73, 73, 73, 20, 8, 1, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 165, 165, 165, 156, 156, 156, 156, 72, 20, 20, 8, 8, 156, 155, 155, 156, 155, 156, 156, 155] 201 rigid atoms, others: [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, 39, 40, 41, 42]) total number of confs: 997 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580794 none COC(=O)C12CCC(C(=O)NCCC3=NC(=O)O[N-]3)(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 4, 4, 4, 32, 53, 155, 155, 155, 155, 155, 1, 1, 1, 1, 7, 7, 7, 1, 1, 1, 1, 4, 32, 32, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 19, 20, 21, 22, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 34, 3, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 30, 31]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580794 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580794 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580794/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580794 Building REAL300025580795 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580795' /scratch/stefan/7787361/working/building/REAL300025580795 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580795 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580795/0 /scratch/stefan/7787361/working/building/REAL300025580795 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/293 `/scratch/stefan/7787361/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC=CC=C2F)=N1) `REAL300025580795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580795 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 11, 29, 29, 40, 40, 40, 114, 116, 201, 201, 201, 201, 201, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 29, 29, 29, 40, 114, 114, 116, 116, 11, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 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]) total number of confs: 599 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580795 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 15, 15, 15, 49, 55, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 11, 11, 1, 11, 11, 12, 1, 8, 8, 8, 8, 8, 8, 15, 49, 49, 55, 55, 1, 11, 11, 11, 11] 201 rigid atoms, others: [1, 37, 14, 15, 16, 17, 18, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580795 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 31, 63, 31, 31, 13, 7, 1, 1, 1, 1, 1, 1, 1, 63, 113, 113, 113, 113, 201, 201, 121, 201, 201, 201, 113, 63, 63, 63, 63, 63, 63, 31, 13, 13, 7, 7, 113, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 829 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580795 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580795 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580795/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580795 Building REAL300025580796 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580796' /scratch/stefan/7787361/working/building/REAL300025580796 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580796 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580796/0 /scratch/stefan/7787361/working/building/REAL300025580796 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/294 `/scratch/stefan/7787361/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC(F)=C2)CCOCC1) `REAL300025580796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580796 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC(F)=C2)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 17, 21, 21, 91, 106, 201, 201, 201, 201, 201, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 21, 91, 91, 106, 106, 3, 3, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17] 201 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, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 591 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580796 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC(F)=C2)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 19, 85, 85, 85, 85, 85, 1, 1, 10, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 15, 15, 19, 19, 10, 10, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580796 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC(F)=C2)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 15, 7, 1, 1, 1, 1, 1, 1, 1, 53, 85, 132, 201, 201, 201, 201, 201, 201, 85, 85, 85, 85, 85, 53, 15, 15, 7, 7, 132, 132, 201, 201, 201, 201, 85, 85, 85, 85, 85, 85, 85, 85] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 680 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580796 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580796 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580796/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580796 Building REAL300025580797 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580797' /scratch/stefan/7787361/working/building/REAL300025580797 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580797 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580797/0 /scratch/stefan/7787361/working/building/REAL300025580797 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/295 `/scratch/stefan/7787361/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(OC2CCCCC2)C(Cl)=C1) `REAL300025580797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580797 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(OC2CCCCC2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 12, 5, 5, 5, 5, 5, 5, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 58, 58, 131, 131, 201, 201, 201, 201, 201, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 58, 131, 131, 131, 131, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 31] 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, 42]) total number of confs: 560 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580797 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(OC2CCCCC2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 12, 5, 5, 5, 5, 5, 5, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 26, 26, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 1, 1, 1, 5, 26, 26, 26, 26, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1] 201 rigid atoms, others: [1, 42, 11, 12, 13, 14, 15, 22, 23, 24, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580797 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(OC2CCCCC2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 12, 5, 5, 5, 5, 5, 5, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 41, 92, 92, 92, 92, 125, 201, 201, 201, 201, 201, 92, 92, 92, 41, 17, 17, 8, 8, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 92] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 589 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580797 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580797 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580797/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580797 Building REAL300025580798 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580798' /scratch/stefan/7787361/working/building/REAL300025580798 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580798 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580798/0 /scratch/stefan/7787361/working/building/REAL300025580798 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/296 `/scratch/stefan/7787361/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C(=O)[C@@H]2CC=CC[C@@H]2C1=O)NCCC1=NC(=O)O[N-]1) `REAL300025580798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580798 none O=C(CN1C(=O)[C@@H]2CC=CC[C@@H]2C1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 201, 201, 201, 201, 201, 201, 52, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580798 none O=C(CN1C(=O)[C@@H]2CC=CC[C@@H]2C1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 94, 98, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 33, 94, 94, 98, 98] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31] set([0, 1, 34, 35, 36, 37, 33, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580798 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580798 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580798/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580798 Building REAL300025580799 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580799' /scratch/stefan/7787361/working/building/REAL300025580799 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580799 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580799/0 /scratch/stefan/7787361/working/building/REAL300025580799 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/297 `/scratch/stefan/7787361/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1) `REAL300025580799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580799 none CC(C)(C)OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 147, 201, 201, 105, 105, 105, 105, 83, 83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 201, 201, 201, 201, 201, 201, 201, 201, 201, 105, 105, 83, 24, 24, 8, 8, 105] 201 rigid atoms, others: [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: 707 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580799 none CC(C)(C)OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 30, 44, 105, 105, 105, 105, 105, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 6, 30, 30, 44, 44, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 38, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 287 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580799 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580799 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580799/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580799 Building REAL300025580800 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580800' /scratch/stefan/7787361/working/building/REAL300025580800 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580800 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580800/0 /scratch/stefan/7787361/working/building/REAL300025580800 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/298 `/scratch/stefan/7787361/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C2=NC=CC=C2C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025580800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580800 none CN1C=C(C2=NC=CC=C2C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 164, 164, 164, 164, 164, 164, 64, 64, 64, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 164, 164, 164, 64, 23, 23, 8, 8, 201] 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]) total number of confs: 427 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580800 none CN1C=C(C2=NC=CC=C2C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 62, 164, 164, 164, 164, 164, 7, 7, 7, 7, 7, 7, 1, 1, 1, 9, 50, 50, 62, 62, 7] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 395 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580800 none CN1C=C(C2=NC=CC=C2C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 29, 29, 29, 105, 113, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 7, 7, 7, 29, 105, 105, 113, 113, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 35, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580800 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580800 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580800/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580800 Building REAL300025580801 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580801' /scratch/stefan/7787361/working/building/REAL300025580801 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580801 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580801/0 /scratch/stefan/7787361/working/building/REAL300025580801 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/299 `/scratch/stefan/7787361/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C12) `REAL300025580801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580801 none CC1=CC(=O)NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [130, 130, 130, 130, 130, 130, 130, 130, 59, 59, 59, 20, 8, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 130, 130, 58, 21, 21, 8, 8, 130, 130] 130 rigid atoms, others: [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]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580801 none CC1=CC(=O)NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 41, 59, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 59, 59, 1, 1] 130 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580801 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580801 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580801/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580801 Building REAL300025580802 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580802' /scratch/stefan/7787361/working/building/REAL300025580802 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580802 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580802/0 /scratch/stefan/7787361/working/building/REAL300025580802 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/300 `/scratch/stefan/7787361/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC=C2Br)CC1) `REAL300025580802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580802 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC=C2Br)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 11, 18, 18, 80, 91, 201, 201, 201, 201, 201, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 18, 80, 80, 91, 91, 5, 5, 1, 1, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 548 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580802 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC=C2Br)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 26, 88, 88, 88, 88, 88, 1, 1, 7, 11, 11, 9, 11, 11, 11, 1, 1, 3, 15, 15, 26, 26, 7, 7, 11, 11, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 33, 11, 12, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580802 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC=C2Br)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 60, 88, 173, 201, 201, 174, 201, 201, 201, 88, 88, 60, 23, 23, 8, 8, 173, 173, 201, 201, 201, 201, 88, 88, 88, 88] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 868 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580802 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580802 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580802/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580802 Building REAL300025580803 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580803' /scratch/stefan/7787361/working/building/REAL300025580803 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580803 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580803/0 /scratch/stefan/7787361/working/building/REAL300025580803 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/301 `/scratch/stefan/7787361/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1C(C(=O)NCCC2=NC(=O)O[N-]2)CCN1C(=O)OC(C)(C)C) `REAL300025580803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580803 none CCC1C(C(=O)NCCC2=NC(=O)O[N-]2)CCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 59, 59, 59, 18, 8, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 118, 118, 201, 201, 201, 201, 63, 63, 63, 63, 63, 63, 63, 58, 19, 19, 8, 8, 63, 63, 63, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 549 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580803 none CCC1C(C(=O)NCCC2=NC(=O)O[N-]2)CCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 4, 4, 4, 12, 18, 63, 63, 63, 63, 63, 1, 1, 1, 1, 6, 6, 18, 23, 23, 23, 3, 3, 3, 3, 3, 1, 1, 4, 12, 12, 18, 18, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [1, 2, 3, 4, 37, 38, 39, 40, 15, 16, 17, 18, 30, 31] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580803 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580803 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580803/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580803 Building REAL300025580804 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580804' /scratch/stefan/7787361/working/building/REAL300025580804 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580804 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580804/0 /scratch/stefan/7787361/working/building/REAL300025580804 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/302 `/scratch/stefan/7787361/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=CSC(C(=O)NCCC3=NC(=O)O[N-]3)=C2N2C=CC=C2)C=C1) `REAL300025580804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580804 none CC1=CC=C(C2=CSC(C(=O)NCCC3=NC(=O)O[N-]3)=C2N2C=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 201, 201, 181, 181, 181, 181, 55, 55, 55, 20, 8, 1, 1, 1, 1, 1, 1, 1, 181, 181, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 55, 21, 21, 8, 8, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 40, 41, 42, 43, 44]) total number of confs: 539 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580804 none CC1=CC=C(C2=CSC(C(=O)NCCC3=NC(=O)O[N-]3)=C2N2C=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 56, 70, 181, 181, 181, 181, 181, 1, 1, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 1, 10, 56, 56, 70, 70, 5, 5, 5, 5, 4, 4] 201 rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 20, 21] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 455 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580804 none CC1=CC=C(C2=CSC(C(=O)NCCC3=NC(=O)O[N-]3)=C2N2C=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 23, 23, 23, 51, 51, 108, 108, 108, 108, 108, 4, 4, 9, 9, 9, 9, 1, 1, 2, 2, 2, 1, 1, 4, 23, 51, 51, 51, 51, 9, 9, 9, 9, 1, 1] 108 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 43, 44, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580804 none CC1=CC=C(C2=CSC(C(=O)NCCC3=NC(=O)O[N-]3)=C2N2C=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [13, 10, 15, 15, 9, 9, 9, 9, 9, 9, 19, 19, 19, 52, 52, 109, 109, 109, 109, 109, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 9, 19, 52, 52, 52, 52, 1, 1, 1, 1, 15, 15] 109 rigid atoms, others: [39, 40, 41, 42, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 316 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580804 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580804 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580804/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580804 Building REAL300025580805 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580805' /scratch/stefan/7787361/working/building/REAL300025580805 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580805 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580805/0 /scratch/stefan/7787361/working/building/REAL300025580805 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/303 `/scratch/stefan/7787361/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC[NH+](C2CCSC2)CC1) `REAL300025580805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580805 none O=C(NCCC1=NC(=O)O[N-]1)C1CC[NH+](C2CCSC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 9, 6, 5, 5, 5, 14, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 4, 33, 33, 107, 129, 201, 201, 201, 201, 201, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 4, 4, 33, 107, 107, 129, 129, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 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, 40, 41, 42, 43]) total number of confs: 624 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580805 none O=C(NCCC1=NC(=O)O[N-]1)C1CC[NH+](C2CCSC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 9, 6, 5, 5, 5, 14, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 69, 91, 168, 168, 168, 168, 168, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 13, 69, 69, 91, 91, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 43, 40, 41, 42, 11, 12, 13, 14, 15, 16, 21, 22, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 495 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580805 none O=C(NCCC1=NC(=O)O[N-]1)C1CC[NH+](C2CCSC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 9, 6, 5, 5, 5, 14, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 17, 8, 1, 1, 1, 1, 1, 1, 1, 81, 168, 168, 168, 168, 168, 201, 201, 201, 201, 168, 168, 81, 17, 17, 8, 8, 168, 168, 168, 168, 168, 201, 201, 201, 201, 201, 201, 201, 168, 168, 168, 168] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 650 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580805 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580805 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580805/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580805 Building REAL300025580806 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580806' /scratch/stefan/7787361/working/building/REAL300025580806 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580806 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580806/0 /scratch/stefan/7787361/working/building/REAL300025580806 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/304 `/scratch/stefan/7787361/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Cl)C=C2NC=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1) `REAL300025580806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580806 none COC1=C(Cl)C=C2NC=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 200, 81, 81, 81, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 80, 22, 22, 8, 8, 201] 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]) total number of confs: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580806 none COC1=C(Cl)C=C2NC=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 55, 71, 200, 200, 200, 200, 200, 1, 1, 4, 4, 4, 1, 1, 1, 9, 55, 55, 72, 72, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 21, 22, 26, 27, 28] set([0, 32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 461 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580806 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580806 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580806/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580806 Building REAL300025580807 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580807' /scratch/stefan/7787361/working/building/REAL300025580807 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580807 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580807/0 /scratch/stefan/7787361/working/building/REAL300025580807 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/305 `/scratch/stefan/7787361/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC=CC=C2)OC1=O) `REAL300025580807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580807 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC=CC=C2)OC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 3, 20, 20, 87, 107, 201, 201, 201, 201, 201, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 20, 87, 87, 107, 107, 3, 3, 3, 3, 1, 1, 1, 1, 1] 201 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: 577 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580807 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC=CC=C2)OC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 57, 79, 201, 201, 201, 201, 201, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 1, 12, 57, 57, 79, 79, 1, 1, 1, 1, 3, 3, 3, 3, 3] 201 rigid atoms, others: [1, 11, 12, 13, 14, 20, 21, 22, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 513 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580807 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC=CC=C2)OC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 24, 23, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 602 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580807 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580807 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580807/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580807 Building REAL300025580808 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580808' /scratch/stefan/7787361/working/building/REAL300025580808 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580808 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580808/0 /scratch/stefan/7787361/working/building/REAL300025580808 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/306 `/scratch/stefan/7787361/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL300025580808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580808 none CC(C)OC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 15, 4, 1, 4, 14, 14, 14, 57, 67, 175, 175, 175, 175, 175, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 4, 14, 57, 57, 67, 67, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 4, 37, 38, 39, 16, 17, 18, 19, 20, 21, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580808 none CC(C)OC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 186, 189, 157, 64, 64, 64, 20, 8, 1, 1, 1, 1, 1, 1, 1, 157, 175, 175, 157, 175, 175, 189, 189, 189, 189, 189, 189, 189, 157, 63, 20, 20, 8, 8, 175, 175, 175, 175, 175] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 785 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580808 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580808 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580808/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580808 Building REAL300025580809 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580809' /scratch/stefan/7787361/working/building/REAL300025580809 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580809 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580809/0 /scratch/stefan/7787361/working/building/REAL300025580809 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/307 `/scratch/stefan/7787361/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC(C2=C(F)C=CC=C2F)=N1) `REAL300025580809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580809 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC(C2=C(F)C=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 10, 29, 29, 45, 45, 45, 113, 120, 201, 201, 201, 201, 201, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 29, 29, 29, 29, 29, 29, 45, 113, 113, 120, 120, 10, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 17, 18, 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, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 636 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580809 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC(C2=C(F)C=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 11, 11, 11, 41, 47, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 5, 5, 5, 5, 5, 5, 11, 41, 41, 47, 47, 1, 7, 7, 7] 201 rigid atoms, others: [1, 38, 14, 15, 16, 17, 18, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580809 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC(C2=C(F)C=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 34, 72, 34, 34, 13, 7, 1, 1, 1, 1, 1, 1, 1, 72, 117, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 117, 72, 72, 72, 72, 72, 72, 34, 13, 13, 7, 7, 117, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580809 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580809 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580809/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580809 Building REAL300025580810 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580810' /scratch/stefan/7787361/working/building/REAL300025580810 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580810 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580810/0 /scratch/stefan/7787361/working/building/REAL300025580810 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/308 `/scratch/stefan/7787361/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2CCCC2)C=C1) `REAL300025580810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580810 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 20, 20, 71, 111, 201, 201, 201, 201, 201, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 20, 71, 71, 111, 111, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39]) total number of confs: 643 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580810 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 17, 31, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 4, 17, 17, 31, 31, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 201 rigid atoms, others: [1, 38, 39, 11, 12, 13, 14, 15, 20, 21, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 218 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580810 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 23, 8, 1, 1, 1, 1, 1, 1, 1, 52, 71, 71, 56, 71, 201, 201, 201, 201, 71, 71, 52, 23, 23, 8, 8, 71, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 71] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 668 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580810 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580810 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580810/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580810 Building REAL300025580811 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580811' /scratch/stefan/7787361/working/building/REAL300025580811 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580811 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580811/0 /scratch/stefan/7787361/working/building/REAL300025580811 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/309 `/scratch/stefan/7787361/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=CC=C2Cl)C1) `REAL300025580811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580811 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=CC=C2Cl)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 2, 12, 12, 56, 89, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 56, 56, 89, 89, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 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, 37, 38]) total number of confs: 545 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580811 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=CC=C2Cl)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 56, 89, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 1, 12, 56, 56, 89, 89, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 1, 37, 38, 11, 12, 13, 14, 15, 22, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 552 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580811 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=CC=C2Cl)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 24, 8, 1, 1, 1, 1, 1, 1, 1, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 584 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580811 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580811 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580811/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580811 Building REAL300025580812 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580812' /scratch/stefan/7787361/working/building/REAL300025580812 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580812 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580812/0 /scratch/stefan/7787361/working/building/REAL300025580812 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/310 `/scratch/stefan/7787361/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2SC(C(=O)NCCC3=NC(=O)O[N-]3)=CC2=C1) `REAL300025580812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580812 none CC1=CC=C2SC(C(=O)NCCC3=NC(=O)O[N-]3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 150, 150, 150, 76, 77, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 151, 151, 151, 150, 150, 76, 24, 24, 8, 8, 150, 150] 151 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]) total number of confs: 369 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580812 none CC1=CC=C2SC(C(=O)NCCC3=NC(=O)O[N-]3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 56, 87, 151, 151, 151, 151, 151, 1, 1, 1, 2, 2, 2, 1, 1, 12, 55, 55, 87, 87, 1, 1] 151 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 32, 24, 25, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580812 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580812 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580812/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580812 Building REAL300025580813 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580813' /scratch/stefan/7787361/working/building/REAL300025580813 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580813 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580813/0 /scratch/stefan/7787361/working/building/REAL300025580813 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/311 `/scratch/stefan/7787361/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1=CC=CC=C1Cl)NCCC1=NC(=O)O[N-]1) `REAL300025580813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580813 none O=C(CCCC1=CC=CC=C1Cl)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 93, 106, 138, 201, 201, 188, 201, 201, 201, 9, 4, 1, 1, 1, 1, 1, 1, 1, 93, 93, 138, 138, 138, 138, 201, 201, 201, 201, 29, 9, 9, 4, 4] 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]) total number of confs: 967 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580813 none O=C(CCCC1=CC=CC=C1Cl)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 105, 105, 201, 201, 201, 201, 201, 11, 11, 5, 5, 5, 5, 1, 1, 1, 1, 39, 105, 105, 105, 105] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580813 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580813 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580813/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580813 Building REAL300025580814 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580814' /scratch/stefan/7787361/working/building/REAL300025580814 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580814 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580814/0 /scratch/stefan/7787361/working/building/REAL300025580814 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/312 `/scratch/stefan/7787361/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)C=C(C)N1CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580814 none CC1=CC(=O)C=C(C)N1CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 162, 43, 43, 43, 18, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 43, 18, 18, 8, 8] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1028 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580814 none CC1=CC(=O)C=C(C)N1CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 26, 26, 26, 103, 105, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 6, 6, 26, 103, 103, 105, 105] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 549 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580814 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580814 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580814/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580814 Building REAL300025580815 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580815' /scratch/stefan/7787361/working/building/REAL300025580815 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580815 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580815/0 /scratch/stefan/7787361/working/building/REAL300025580815 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/313 `/scratch/stefan/7787361/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=CC=C2F)C1) `REAL300025580815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580815 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=CC=C2F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 5, 29, 29, 98, 101, 201, 201, 201, 201, 201, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 29, 98, 98, 101, 101, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [33, 34, 35, 36, 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, 37, 38]) total number of confs: 552 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580815 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=CC=C2F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 38, 41, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 5, 5, 3, 5, 5, 5, 1, 9, 38, 38, 41, 41, 1, 1, 1, 1, 1, 5, 5, 4, 5, 1, 1] 201 rigid atoms, others: [32, 1, 37, 38, 11, 12, 13, 14, 15, 22, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 249 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580815 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=CC=C2F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 18, 8, 1, 1, 1, 1, 1, 1, 1, 40, 96, 96, 96, 96, 201, 201, 147, 201, 201, 201, 96, 40, 18, 18, 8, 8, 96, 96, 96, 96, 96, 201, 201, 201, 201, 96, 96] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 661 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580815 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580815 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580815/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580815 Building REAL300025580816 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580816' /scratch/stefan/7787361/working/building/REAL300025580816 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580816 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580816/0 /scratch/stefan/7787361/working/building/REAL300025580816 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/314 `/scratch/stefan/7787361/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl) `REAL300025580816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580816 none CC(C)(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 119, 119, 119, 119, 51, 51, 51, 21, 8, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 50, 22, 22, 8, 8, 119] 119 rigid atoms, others: [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: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580816 none CC(C)(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 41, 60, 119, 119, 119, 119, 119, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 7, 41, 41, 60, 60, 1] 119 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 19, 20, 21, 38, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580816 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580816 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580816/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580816 Building REAL300025580817 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580817' /scratch/stefan/7787361/working/building/REAL300025580817 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580817 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580817/0 /scratch/stefan/7787361/working/building/REAL300025580817 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/315 `/scratch/stefan/7787361/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C(=O)C(F)(F)OC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1) `REAL300025580817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580817 none O=C(CN1C(=O)C(F)(F)OC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 184, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 20, 8, 1, 1, 1, 1, 1, 1, 1, 184, 184, 201, 201, 201, 201, 61, 21, 21, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 733 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580817 none O=C(CN1C(=O)C(F)(F)OC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 81, 97, 201, 201, 201, 201, 201, 3, 3, 1, 1, 1, 1, 22, 81, 81, 97, 97] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 34, 35, 33, 32, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 561 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580817 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580817 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580817/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580817 Building REAL300025580818 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580818' /scratch/stefan/7787361/working/building/REAL300025580818 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580818 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580818/0 /scratch/stefan/7787361/working/building/REAL300025580818 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/316 `/scratch/stefan/7787361/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025580818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580818 none CC(C)(C)OC(=O)N1CCC([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 152, 107, 152, 107, 107, 107, 100, 100, 100, 100, 37, 100, 37, 37, 9, 9, 1, 1, 1, 1, 1, 1, 1, 107, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 107, 107, 107, 107, 100, 100, 37, 9, 9, 9, 9, 107, 107, 107, 107] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 570 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580818 none CC(C)(C)OC(=O)N1CCC([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 7, 4, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 40, 40, 100, 100, 100, 100, 100, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 4, 1, 1, 11, 40, 40, 40, 40, 4, 4, 4, 4] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580818 none CC(C)(C)OC(=O)N1CCC([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 30, 30, 30, 56, 56, 107, 107, 107, 107, 107, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 1, 1, 1, 1, 4, 4, 30, 56, 56, 56, 56, 1, 1, 1, 1] 201 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 40, 50, 51, 52, 53, 41, 27, 28, 42] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580818 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580818 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580818/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580818 Building REAL300025580819 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580819' /scratch/stefan/7787361/working/building/REAL300025580819 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580819 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580819/0 /scratch/stefan/7787361/working/building/REAL300025580819 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/317 `/scratch/stefan/7787361/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C(Br)S1) `REAL300025580819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580819 none CC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C(Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 105, 105, 105, 24, 8, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 172, 172, 105, 24, 24, 8, 8] 172 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]) total number of confs: 414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580819 none CC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C(Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 7, 7, 7, 34, 63, 172, 172, 172, 172, 172, 1, 1, 1, 2, 2, 2, 7, 34, 34, 63, 63] 172 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580819 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580819 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580819/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580819 Building REAL300025580820 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580820' /scratch/stefan/7787361/working/building/REAL300025580820 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580820 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580820/0 /scratch/stefan/7787361/working/building/REAL300025580820 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/318 `/scratch/stefan/7787361/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C2OCOC2=C1) `REAL300025580820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580820 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 30, 30, 30, 100, 105, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 30, 100, 100, 105, 105, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 577 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580820 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 112, 42, 42, 16, 7, 1, 1, 1, 1, 1, 1, 1, 112, 201, 201, 201, 201, 201, 201, 201, 201, 112, 112, 112, 112, 112, 112, 42, 16, 16, 7, 7, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580820 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580820 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580820/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580820 Building REAL300025580821 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580821' /scratch/stefan/7787361/working/building/REAL300025580821 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580821 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580821/0 /scratch/stefan/7787361/working/building/REAL300025580821 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/319 `/scratch/stefan/7787361/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C2=CC=C(Cl)C=C2)=N1) `REAL300025580821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580821 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C2=CC=C(Cl)C=C2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 39, 39, 112, 133, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 39, 112, 112, 133, 133, 6, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 624 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580821 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C2=CC=C(Cl)C=C2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 39, 60, 199, 199, 199, 199, 199, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 6, 1, 12, 39, 39, 60, 60, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 23, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 457 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580821 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C2=CC=C(Cl)C=C2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 101, 199, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 199, 101, 24, 24, 8, 8, 199, 199, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580821 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580821 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580821/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580821 Building REAL300025580822 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580822' /scratch/stefan/7787361/working/building/REAL300025580822 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580822 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580822/0 /scratch/stefan/7787361/working/building/REAL300025580822 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/320 `/scratch/stefan/7787361/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C(F)(F)F)=C1) `REAL300025580822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580822 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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: [5, 1, 5, 5, 32, 57, 136, 136, 136, 136, 136, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 32, 32, 57, 57, 1, 1, 1] 136 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 376 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580822 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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: [66, 66, 22, 8, 1, 1, 1, 1, 1, 1, 1, 66, 136, 136, 102, 136, 136, 136, 136, 136, 136, 65, 22, 22, 8, 8, 136, 136, 136] 136 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580822 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580822 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580822/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580822 Building REAL300025580823 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580823' /scratch/stefan/7787361/working/building/REAL300025580823 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580823 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580823/0 /scratch/stefan/7787361/working/building/REAL300025580823 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/321 `/scratch/stefan/7787361/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=N1) `REAL300025580823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580823 none CC1=CSC(NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 194, 38, 38, 98, 98, 38, 38, 38, 15, 7, 1, 1, 1, 1, 1, 1, 1, 98, 98, 201, 201, 201, 201, 201, 194, 98, 98, 38, 15, 15, 7, 7, 98, 98] 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]) total number of confs: 727 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580823 none CC1=CSC(NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 24, 98, 98, 98, 98, 98, 1, 1, 12, 12, 12, 12, 12, 6, 1, 1, 5, 23, 23, 24, 24, 1, 1] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 21, 22, 29, 30, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580823 none CC1=CSC(NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 12, 12, 7, 7, 39, 39, 39, 121, 121, 201, 201, 201, 201, 201, 12, 12, 1, 2, 2, 2, 1, 7, 12, 12, 39, 121, 121, 121, 121, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 600 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580823 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580823 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580823/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580823 Building REAL300025580824 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580824' /scratch/stefan/7787361/working/building/REAL300025580824 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580824 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580824/0 /scratch/stefan/7787361/working/building/REAL300025580824 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/322 `/scratch/stefan/7787361/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=NC(N2CCOCC2)=N1) `REAL300025580824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580824 none NC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=NC(N2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 8, 5, 5, 12, 5, 5, 8, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 11, 38, 38, 38, 113, 121, 201, 201, 201, 201, 201, 10, 1, 1, 1, 1, 1, 1, 1, 10, 11, 11, 37, 113, 113, 121, 121, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 31] 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]) total number of confs: 595 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580824 none NC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=NC(N2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 8, 5, 5, 12, 5, 5, 8, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 61, 61, 61, 20, 8, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 201, 201, 201, 201, 201, 61, 139, 139, 61, 20, 20, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201] 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, 34, 35, 36, 37, 38]) total number of confs: 584 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580824 none NC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=NC(N2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 8, 5, 5, 12, 5, 5, 8, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 35, 42, 139, 139, 139, 139, 139, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 1, 6, 35, 35, 42, 42, 10, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580824 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580824 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580824/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580824 Building REAL300025580825 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580825' /scratch/stefan/7787361/working/building/REAL300025580825 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580825 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580825/0 /scratch/stefan/7787361/working/building/REAL300025580825 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/323 `/scratch/stefan/7787361/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(OCC(F)F)C=N1) `REAL300025580825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580825 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(OCC(F)F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 12, 5, 5, 15, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 14, 19, 82, 81, 81, 81, 82, 1, 1, 1, 1, 1, 3, 13, 34, 34, 1, 1, 3, 13, 13, 20, 20, 1, 13, 13, 34, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 20, 21, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580825 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(OCC(F)F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 12, 5, 5, 15, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 1, 1, 1, 1, 1, 1, 1, 71, 82, 82, 82, 82, 141, 198, 201, 201, 82, 82, 70, 21, 21, 7, 7, 82, 198, 198, 201, 82] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 684 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580825 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580825 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580825/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580825 Building REAL300025580826 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580826' /scratch/stefan/7787361/working/building/REAL300025580826 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580826 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580826/0 /scratch/stefan/7787361/working/building/REAL300025580826 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/324 `/scratch/stefan/7787361/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2CCOCC2)N=N1) `REAL300025580826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580826 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2CCOCC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 11, 44, 44, 108, 120, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 44, 108, 108, 120, 120, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 566 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580826 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2CCOCC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 32, 38, 92, 92, 92, 93, 93, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 8, 31, 31, 38, 38, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [1, 11, 12, 13, 14, 20, 21, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580826 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2CCOCC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 20, 8, 1, 1, 1, 1, 1, 1, 1, 54, 93, 93, 93, 201, 201, 201, 201, 201, 92, 92, 53, 20, 20, 8, 8, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 560 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580826 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580826 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580826/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580826 Building REAL300025580827 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580827' /scratch/stefan/7787361/working/building/REAL300025580827 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580827 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580827/0 /scratch/stefan/7787361/working/building/REAL300025580827 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/325 `/scratch/stefan/7787361/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CC=C2C=C1Cl) `REAL300025580827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580827 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CC=C2C=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 39, 63, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 63, 63, 1, 1, 1, 1, 1] 137 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 389 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580827 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CC=C2C=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 24, 8, 1, 1, 1, 1, 1, 1, 1, 87, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 87, 24, 24, 8, 8, 137, 137, 137, 137, 137] 137 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580827 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580827 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580827/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580827 Building REAL300025580828 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580828' /scratch/stefan/7787361/working/building/REAL300025580828 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580828 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580828/0 /scratch/stefan/7787361/working/building/REAL300025580828 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/326 `/scratch/stefan/7787361/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2SC(C(=O)NCCC3=NC(=O)O[N-]3)=CC2=CC=C1) `REAL300025580828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580828 none CC1=C2SC(C(=O)NCCC3=NC(=O)O[N-]3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 98, 98, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 166, 166, 166, 166, 166, 166, 166, 166, 98, 24, 24, 8, 8, 166, 166, 166, 166] 166 rigid atoms, others: [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]) total number of confs: 409 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580828 none CC1=C2SC(C(=O)NCCC3=NC(=O)O[N-]3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 68, 97, 166, 166, 166, 166, 166, 1, 1, 1, 1, 1, 2, 2, 2, 12, 67, 67, 97, 97, 1, 1, 1, 1] 166 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 16, 17, 18, 19, 20, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580828 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580828 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580828/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580828 Building REAL300025580829 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580829' /scratch/stefan/7787361/working/building/REAL300025580829 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580829 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580829/0 /scratch/stefan/7787361/working/building/REAL300025580829 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/327 `/scratch/stefan/7787361/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC(Br)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580829 none CN1N=NC(Br)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 171, 171, 171, 111, 111, 111, 22, 8, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 111, 22, 22, 8, 8] 171 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]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580829 none CN1N=NC(Br)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 63, 171, 171, 171, 171, 171, 2, 2, 2, 7, 37, 37, 63, 63] 171 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580829 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580829 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580829/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580829 Building REAL300025580830 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580830' /scratch/stefan/7787361/working/building/REAL300025580830 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580830 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580830/0 /scratch/stefan/7787361/working/building/REAL300025580830 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/328 `/scratch/stefan/7787361/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=C(C(F)(F)F)C=C1F) `REAL300025580830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580830 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=C(C(F)(F)F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 80, 113, 180, 180, 180, 180, 180, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 12, 79, 79, 113, 113, 1, 1] 180 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 20, 21, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 568 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580830 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=C(C(F)(F)F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [118, 118, 24, 8, 1, 1, 1, 1, 1, 1, 1, 118, 180, 180, 180, 180, 180, 180, 180, 180, 180, 180, 180, 117, 24, 24, 8, 8, 180, 180] 180 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580830 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580830 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580830/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580830 Building REAL300025580831 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580831' /scratch/stefan/7787361/working/building/REAL300025580831 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580831 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580831/0 /scratch/stefan/7787361/working/building/REAL300025580831 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/329 `/scratch/stefan/7787361/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC=C(Cl)C=C2Cl)=NO1) `REAL300025580831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580831 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC=C(Cl)C=C2Cl)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 37, 107, 115, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 37, 107, 107, 115, 115, 10, 10, 10, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 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]) total number of confs: 570 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580831 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC=C(Cl)C=C2Cl)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 41, 52, 140, 140, 140, 140, 140, 1, 1, 1, 1, 10, 10, 1, 2, 10, 10, 10, 1, 1, 11, 41, 41, 52, 52, 1, 1, 1, 10, 10, 10] 201 rigid atoms, others: [1, 11, 12, 13, 14, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580831 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(C2=CC=C(Cl)C=C2Cl)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 1, 1, 1, 1, 1, 1, 1, 73, 140, 140, 140, 201, 201, 140, 201, 201, 201, 201, 140, 140, 73, 21, 21, 8, 8, 140, 140, 140, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 815 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580831 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580831 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580831/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580831 Building REAL300025580832 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580832' /scratch/stefan/7787361/working/building/REAL300025580832 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580832 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580832/0 /scratch/stefan/7787361/working/building/REAL300025580832 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/330 `/scratch/stefan/7787361/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)CCCC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580832 none COC1=CC=C(C(=O)CCCC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 109, 201, 79, 95, 61, 61, 61, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 105, 105, 95, 95, 95, 95, 61, 17, 17, 8, 8, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 816 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580832 none COC1=CC=C(C(=O)CCCC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 18, 21, 32, 32, 32, 86, 86, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 16, 16, 18, 18, 21, 21, 32, 86, 86, 86, 86, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 41, 22, 23, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 543 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580832 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580832 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580832/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580832 Building REAL300025580833 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580833' /scratch/stefan/7787361/working/building/REAL300025580833 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580833 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580833/0 /scratch/stefan/7787361/working/building/REAL300025580833 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/331 `/scratch/stefan/7787361/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1NC(=O)C=C2) `REAL300025580833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580833 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1NC(=O)C=C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [10, 1, 10, 10, 48, 69, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 48, 48, 69, 69, 1, 1, 1, 1, 1, 1] 159 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580833 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1NC(=O)C=C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [69, 69, 21, 8, 1, 1, 1, 1, 1, 1, 1, 69, 159, 159, 159, 159, 159, 159, 159, 159, 159, 159, 68, 21, 21, 8, 8, 159, 159, 159, 159, 159, 159] 159 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580833 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580833 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580833/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580833 Building REAL300025580834 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580834' /scratch/stefan/7787361/working/building/REAL300025580834 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580834 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580834/0 /scratch/stefan/7787361/working/building/REAL300025580834 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/332 `/scratch/stefan/7787361/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580834 none CC(C)[C@@H](NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 109, 123, 33, 109, 109, 148, 191, 191, 199, 199, 199, 199, 32, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 127, 127, 148, 199, 199, 199, 199, 199, 199, 199, 199, 199, 32, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 874 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580834 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580834 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580834/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580834 Building REAL300025580835 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580835' /scratch/stefan/7787361/working/building/REAL300025580835 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580835 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580835/0 /scratch/stefan/7787361/working/building/REAL300025580835 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/333 `/scratch/stefan/7787361/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCN(C(=O)OC(C)(C)C)C1) `REAL300025580835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580835 none COCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 8, 8, 8, 8, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 8, 10, 10, 10, 10, 10, 8, 7, 7, 5, 5, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8] 17 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580835 none COCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 8, 8, 8, 8, 8, 1, 1, 1, 1, 2, 2, 4, 4, 5, 4, 1, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 17 rigid atoms, others: [2, 3, 4, 37, 38, 39, 50, 15, 16, 17, 18, 25, 49, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580835 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580835 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580835/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580835 Building REAL300025580836 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580836' /scratch/stefan/7787361/working/building/REAL300025580836 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580836 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580836/0 /scratch/stefan/7787361/working/building/REAL300025580836 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/334 `/scratch/stefan/7787361/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CC=C2C=C1Br) `REAL300025580836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580836 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CC=C2C=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 39, 61, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 61, 61, 1, 1, 1, 1, 1] 130 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 374 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580836 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CC=C2C=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 76, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 76, 24, 24, 8, 8, 130, 130, 130, 130, 130] 130 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580836 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580836 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580836/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580836 Building REAL300025580837 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580837' /scratch/stefan/7787361/working/building/REAL300025580837 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580837 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580837/0 /scratch/stefan/7787361/working/building/REAL300025580837 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/335 `/scratch/stefan/7787361/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](OC1=CC=C(Cl)C2=CC=CC=C12)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580837 none C[C@H](OC1=CC=C(Cl)C2=CC=CC=C12)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 34, 94, 94, 155, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 34, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 94, 94, 88, 201, 201, 201, 201, 201, 201, 33, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 536 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580837 none C[C@H](OC1=CC=C(Cl)C2=CC=CC=C12)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 52, 52, 52, 99, 99, 201, 201, 201, 201, 201, 14, 14, 14, 1, 1, 1, 1, 1, 1, 52, 99, 99, 99, 99] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39]) total number of confs: 555 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580837 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580837 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580837/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580837 Building REAL300025580838 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580838' /scratch/stefan/7787361/working/building/REAL300025580838 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580838 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580838/0 /scratch/stefan/7787361/working/building/REAL300025580838 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/336 `/scratch/stefan/7787361/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2NC(=O)CSC2=C1) `REAL300025580838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580838 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2NC(=O)CSC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 37, 61, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 61, 61, 1, 1, 1, 1, 1, 1] 116 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 345 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580838 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2NC(=O)CSC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [57, 56, 22, 8, 1, 1, 1, 1, 1, 1, 1, 56, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 56, 22, 22, 8, 8, 116, 116, 116, 116, 116, 116] 116 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580838 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580838 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580838/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580838 Building REAL300025580839 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580839' /scratch/stefan/7787361/working/building/REAL300025580839 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580839 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580839/0 /scratch/stefan/7787361/working/building/REAL300025580839 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/337 `/scratch/stefan/7787361/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)NCCC2=NC(=O)O[N-]2)CCCN1C(=O)OC(C)(C)C) `REAL300025580839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580839 none CC1C(C(=O)NCCC2=NC(=O)O[N-]2)CCCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 41, 41, 41, 19, 8, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 192, 192, 201, 201, 201, 201, 83, 83, 83, 83, 83, 41, 19, 19, 8, 8, 83, 83, 83, 83, 83, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580839 none CC1C(C(=O)NCCC2=NC(=O)O[N-]2)CCCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 29, 33, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 2, 2, 2, 1, 1, 7, 29, 29, 33, 33, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580839 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580839 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580839/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580839 Building REAL300025580840 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580840' /scratch/stefan/7787361/working/building/REAL300025580840 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580840 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580840/0 /scratch/stefan/7787361/working/building/REAL300025580840 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/338 `/scratch/stefan/7787361/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C12CCC(C(F)(F)F)(CC1)CC2) `REAL300025580840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580840 none O=C(NCCC1=NC(=O)O[N-]1)C12CCC(C(F)(F)F)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 27, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 3, 15, 15, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 48 rigid atoms, others: [1, 11, 12, 13, 14, 15, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580840 none O=C(NCCC1=NC(=O)O[N-]1)C12CCC(C(F)(F)F)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 21, 8, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 21, 21, 8, 8, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48] 48 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580840 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580840 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580840/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580840 Building REAL300025580841 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580841' /scratch/stefan/7787361/working/building/REAL300025580841 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580841 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580841/0 /scratch/stefan/7787361/working/building/REAL300025580841 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/339 `/scratch/stefan/7787361/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1[N+](=O)[O-]) `REAL300025580841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580841 none CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 201, 201, 119, 47, 47, 47, 16, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 47, 16, 16, 8, 8, 201] 201 rigid atoms, others: [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]) total number of confs: 1152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580841 none CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 83, 91, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 6, 6, 17, 83, 83, 91, 91, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 17, 18, 19, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 549 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580841 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580841 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580841/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580841 Building REAL300025580842 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580842' /scratch/stefan/7787361/working/building/REAL300025580842 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580842 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580842/0 /scratch/stefan/7787361/working/building/REAL300025580842 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/340 `/scratch/stefan/7787361/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)COC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21) `REAL300025580842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580842 none CC1(C)COC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 125, 125, 125, 125, 58, 58, 58, 22, 8, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 57, 23, 23, 8, 8, 125] 125 rigid atoms, others: [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: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580842 none CC1(C)COC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 34, 56, 125, 125, 125, 125, 125, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 34, 34, 56, 56, 1] 125 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 37, 20, 21, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580842 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580842 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580842/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580842 Building REAL300025580843 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580843' /scratch/stefan/7787361/working/building/REAL300025580843 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580843 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580843/0 /scratch/stefan/7787361/working/building/REAL300025580843 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/341 `/scratch/stefan/7787361/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC(F)=CC=C2F)=N1) `REAL300025580843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580843 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC(F)=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 13, 28, 28, 35, 35, 35, 117, 125, 201, 201, 201, 201, 201, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 28, 28, 28, 28, 28, 28, 35, 117, 117, 125, 125, 13, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 17, 18, 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, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 634 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580843 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC(F)=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 38, 42, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 13, 13, 13, 12, 13, 13, 13, 1, 6, 6, 6, 6, 6, 6, 12, 38, 38, 42, 42, 1, 13, 12, 13] 201 rigid atoms, others: [1, 38, 14, 15, 16, 17, 18, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580843 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC(F)=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 28, 58, 28, 28, 11, 7, 1, 1, 1, 1, 1, 1, 1, 58, 94, 94, 94, 94, 201, 201, 201, 201, 201, 201, 201, 94, 58, 58, 58, 58, 58, 58, 28, 11, 11, 7, 7, 94, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 479 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580843 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580843 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580843/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580843 Building REAL300025580844 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580844' /scratch/stefan/7787361/working/building/REAL300025580844 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580844 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580844/0 /scratch/stefan/7787361/working/building/REAL300025580844 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/342 `/scratch/stefan/7787361/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC=C1C1=NC(C(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)=CS1) `REAL300025580844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580844 none CC1=CC(F)=CC=C1C1=NC(C(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 161, 201, 201, 105, 105, 105, 55, 31, 55, 55, 31, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 201, 201, 201, 201, 201, 201, 55, 55, 55, 55, 55, 55, 31, 8, 8, 8, 8, 105] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 803 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580844 none CC1=CC(F)=CC=C1C1=NC(C(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 1, 1, 10, 10, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 43, 43, 105, 105, 105, 105, 105, 1, 1, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 17, 43, 43, 43, 43, 1] 201 rigid atoms, others: [7, 8, 9, 10, 11, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580844 none CC1=CC(F)=CC=C1C1=NC(C(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 41, 41, 41, 55, 55, 55, 95, 95, 201, 201, 201, 201, 201, 10, 10, 2, 2, 2, 1, 1, 1, 41, 41, 41, 41, 41, 41, 55, 95, 95, 95, 95, 10] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 567 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580844 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580844 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580844/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580844 Building REAL300025580845 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580845' /scratch/stefan/7787361/working/building/REAL300025580845 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580845 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580845/0 /scratch/stefan/7787361/working/building/REAL300025580845 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/343 `/scratch/stefan/7787361/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC2=C(C(=O)NCCC3=NC(=O)O[N-]3)NN=C21) `REAL300025580845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580845 none COC1=CC=CC2=C(C(=O)NCCC3=NC(=O)O[N-]3)NN=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 200, 201, 201, 201, 201, 201, 201, 201, 83, 23, 23, 8, 8, 201] 201 rigid atoms, others: [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: 425 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580845 none COC1=CC=CC2=C(C(=O)NCCC3=NC(=O)O[N-]3)NN=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 52, 71, 201, 201, 201, 201, 201, 1, 1, 1, 4, 4, 4, 1, 1, 1, 10, 52, 52, 71, 71, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 33, 19, 20, 21, 25, 26, 27] set([0, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 466 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580845 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580845 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580845/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580845 Building REAL300025580846 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580846' /scratch/stefan/7787361/working/building/REAL300025580846 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580846 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580846/0 /scratch/stefan/7787361/working/building/REAL300025580846 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/344 `/scratch/stefan/7787361/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC(Cl)=C2)CCCCC1) `REAL300025580846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580846 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC(Cl)=C2)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 17, 23, 23, 99, 109, 201, 201, 201, 201, 201, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 23, 99, 99, 109, 109, 3, 3, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 201 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 579 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580846 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC(Cl)=C2)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 17, 78, 78, 78, 78, 78, 1, 1, 10, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 15, 15, 17, 17, 10, 10, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 45, 44, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 182 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580846 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC(Cl)=C2)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 1, 1, 1, 1, 1, 1, 1, 47, 78, 133, 201, 201, 201, 201, 201, 201, 78, 78, 78, 78, 78, 47, 15, 15, 7, 7, 133, 133, 201, 201, 201, 201, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 710 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580846 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580846 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580846/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580846 Building REAL300025580847 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580847' /scratch/stefan/7787361/working/building/REAL300025580847 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580847 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580847/0 /scratch/stefan/7787361/working/building/REAL300025580847 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/345 `/scratch/stefan/7787361/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(C(F)C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025580847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580847 none CC(C)(C)OC(=O)N1CC(C(F)C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 160, 140, 160, 140, 140, 85, 43, 87, 43, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 140, 140, 87, 43, 8, 8, 8, 8, 140, 140] 201 rigid atoms, others: [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: 642 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580847 none CC(C)(C)OC(=O)N1CC(C(F)C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 8, 9, 9, 2, 1, 2, 1, 1, 1, 1, 7, 7, 28, 28, 28, 78, 78, 140, 140, 140, 140, 140, 1, 10, 10, 10, 9, 9, 9, 10, 10, 10, 1, 1, 1, 7, 28, 78, 78, 78, 78, 1, 1] 201 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 43, 23, 42] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580847 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580847 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580847/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580847 Building REAL300025580848 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580848' /scratch/stefan/7787361/working/building/REAL300025580848 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580848 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580848/0 /scratch/stefan/7787361/working/building/REAL300025580848 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/346 `/scratch/stefan/7787361/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CS2)CCCCC1) `REAL300025580848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580848 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CS2)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 15, 21, 21, 88, 98, 201, 201, 201, 201, 201, 3, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 21, 88, 88, 98, 98, 3, 3, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 30, 31] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 548 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580848 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CS2)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 21, 94, 94, 94, 94, 94, 1, 1, 10, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 15, 15, 21, 21, 10, 10, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 38, 33, 40, 41, 42, 11, 12, 18, 19, 20, 21, 22, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580848 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CS2)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 56, 94, 140, 201, 201, 201, 201, 94, 94, 94, 94, 94, 56, 19, 19, 8, 8, 140, 140, 201, 201, 201, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 738 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580848 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580848 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580848/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580848 Building REAL300025580849 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580849' /scratch/stefan/7787361/working/building/REAL300025580849 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580849 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580849/0 /scratch/stefan/7787361/working/building/REAL300025580849 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/347 `/scratch/stefan/7787361/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)=C1) `REAL300025580849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580849 none CC1=NOC(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 187, 116, 116, 116, 116, 64, 64, 64, 21, 8, 1, 1, 1, 1, 1, 1, 1, 116, 116, 201, 201, 201, 201, 187, 187, 63, 21, 21, 8, 8, 116, 116, 116, 201] 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]) total number of confs: 685 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580849 none CC1=NOC(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 36, 49, 116, 116, 116, 116, 116, 1, 1, 15, 15, 15, 15, 4, 4, 10, 36, 36, 49, 49, 2, 2, 2, 15] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 21, 22] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 343 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580849 none CC1=NOC(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 15, 15, 15, 15, 47, 47, 47, 116, 133, 201, 201, 201, 201, 201, 15, 15, 1, 2, 2, 2, 8, 8, 47, 116, 116, 133, 133, 15, 15, 15, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 663 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580849 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580849 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580849/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580849 Building REAL300025580850 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580850' /scratch/stefan/7787361/working/building/REAL300025580850 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580850 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580850/0 /scratch/stefan/7787361/working/building/REAL300025580850 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/348 `/scratch/stefan/7787361/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Br) `REAL300025580850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580850 none CC1=CC(C(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 89, 37, 89, 89, 37, 37, 13, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 179, 195, 201, 201, 201, 201, 89, 89, 89, 89, 89, 89, 37, 13, 13, 7, 7, 201, 201] 201 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, 37, 38]) total number of confs: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580850 none CC1=CC(C(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 31, 31, 31, 108, 112, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 13, 13, 13, 13, 13, 13, 31, 108, 108, 112, 112, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580850 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580850 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580850/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580850 Building REAL300025580851 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580851' /scratch/stefan/7787361/working/building/REAL300025580851 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580851 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580851/0 /scratch/stefan/7787361/working/building/REAL300025580851 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/349 `/scratch/stefan/7787361/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580851 none CCOC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 188, 183, 51, 183, 51, 136, 136, 51, 51, 51, 19, 8, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 201, 201, 201, 136, 136, 51, 19, 19, 8, 8, 136, 136] 201 rigid atoms, others: [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]) total number of confs: 881 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580851 none CCOC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 5, 1, 5, 1, 1, 1, 1, 1, 5, 5, 5, 29, 36, 136, 136, 136, 136, 136, 1, 1, 28, 28, 28, 27, 27, 1, 1, 5, 29, 29, 36, 36, 1, 1] 201 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 35, 20, 21, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580851 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580851 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580851/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580851 Building REAL300025580852 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580852' /scratch/stefan/7787361/working/building/REAL300025580852 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580852 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580852/0 /scratch/stefan/7787361/working/building/REAL300025580852 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/350 `/scratch/stefan/7787361/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC2=CC(F)=CC=C21) `REAL300025580852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580852 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC2=CC(F)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 91, 91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 149, 149, 149, 149, 149, 149, 149, 91, 24, 24, 8, 8, 149, 149, 149] 149 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 377 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580852 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC2=CC(F)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 7, 7, 7, 47, 73, 149, 149, 149, 149, 149, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 47, 47, 73, 73, 1, 1, 1] 149 rigid atoms, others: [0, 1, 2, 3, 32, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580852 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580852 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580852/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580852 Building REAL300025580853 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580853' /scratch/stefan/7787361/working/building/REAL300025580853 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025580853 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580853/0 /scratch/stefan/7787361/working/building/REAL300025580853 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/351 `/scratch/stefan/7787361/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C=NC2=C(Br)C=CC=C21) `REAL300025580853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580853 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C=NC2=C(Br)C=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 8, 1, 1, 17, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 396 conformations in input total number of sets (complete confs): 396 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 54, 87, 198, 198, 198, 198, 198, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 54, 54, 87, 87, 2, 1, 1, 1, 1] 396 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28]) total number of confs: 542 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580853 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C=NC2=C(Br)C=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 8, 1, 1, 17, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 396 conformations in input total number of sets (complete confs): 396 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 24, 8, 1, 1, 1, 1, 1, 1, 1, 100, 198, 198, 198, 198, 198, 198, 198, 198, 198, 198, 198, 100, 24, 24, 8, 8, 396, 198, 198, 198, 198] 396 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 829 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580853 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025580853/1 /scratch/stefan/7787361/working/building/REAL300025580853 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/352 `/scratch/stefan/7787361/working/3D/352' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C([O-])C=NC2=C(Br)C=CC=C21) `REAL300025580853.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025580853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580853 none O=C(NCCC1=NC(=O)O[N-]1)C1=C([O-])C=NC2=C(Br)C=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 8, 1, 1, 17, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 32, 39, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 32, 32, 39, 39, 1, 1, 1, 1] 68 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580853 none O=C(NCCC1=NC(=O)O[N-]1)C1=C([O-])C=NC2=C(Br)C=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 8, 1, 1, 17, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 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: [54, 54, 20, 8, 1, 1, 1, 1, 1, 1, 1, 54, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 54, 20, 20, 8, 8, 68, 68, 68, 68] 68 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580853 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580853 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025580853/1.* 0: /scratch/stefan/7787361/working/building/REAL300025580853/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580853 Building REAL300025580854 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580854' /scratch/stefan/7787361/working/building/REAL300025580854 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580854 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580854/0 /scratch/stefan/7787361/working/building/REAL300025580854 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/353 `/scratch/stefan/7787361/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=NC(C2=CC=CC=C2)=C1) `REAL300025580854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580854 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=NC(C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 21, 95, 106, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 21, 95, 95, 106, 106, 6, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 548 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580854 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=NC(C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 37, 156, 156, 156, 156, 156, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 5, 29, 29, 37, 37, 1, 6, 6, 1, 6, 6, 1] 201 rigid atoms, others: [1, 34, 11, 12, 13, 14, 15, 16, 22, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580854 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=NC(C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 19, 8, 1, 1, 1, 1, 1, 1, 1, 67, 156, 156, 156, 156, 156, 201, 201, 156, 201, 201, 156, 67, 19, 19, 8, 8, 156, 201, 201, 156, 201, 201, 156] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580854 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580854 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580854/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580854 Building REAL300025580855 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580855' /scratch/stefan/7787361/working/building/REAL300025580855 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580855 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580855/0 /scratch/stefan/7787361/working/building/REAL300025580855 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/354 `/scratch/stefan/7787361/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CN=C1C1=CC=CC=C1) `REAL300025580855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580855 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CN=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 4, 22, 22, 80, 104, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 22, 80, 80, 104, 104, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 571 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580855 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CN=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 53, 80, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 10, 53, 53, 80, 80, 1, 1, 4, 4, 2, 4, 4] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 516 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580855 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CN=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 148, 201, 201, 201, 201, 201, 201, 201, 201, 73, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580855 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580855 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580855/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580855 Building REAL300025580856 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580856' /scratch/stefan/7787361/working/building/REAL300025580856 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580856 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580856/0 /scratch/stefan/7787361/working/building/REAL300025580856 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/355 `/scratch/stefan/7787361/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=C(C(=O)NCCC3=NC(=O)O[N-]3)N=CO2)C=C1) `REAL300025580856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580856 none COC1=CC=C(C2=C(C(=O)NCCC3=NC(=O)O[N-]3)N=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 138, 138, 78, 79, 79, 24, 8, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 201, 201, 201, 201, 201, 201, 201, 78, 25, 25, 8, 8, 138, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 470 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580856 none COC1=CC=C(C2=C(C(=O)NCCC3=NC(=O)O[N-]3)N=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 2, 7, 7, 1, 1, 1, 1, 10, 10, 10, 36, 46, 138, 138, 138, 138, 138, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 10, 36, 36, 46, 46, 1, 7, 7] 201 rigid atoms, others: [34, 5, 6, 7, 8, 19, 20, 21] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580856 none COC1=CC=C(C2=C(C(=O)NCCC3=NC(=O)O[N-]3)N=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 87, 102, 201, 201, 201, 201, 201, 7, 7, 7, 1, 1, 1, 2, 2, 1, 1, 31, 87, 87, 102, 102, 7, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 22, 23, 24, 36, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 553 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580856 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580856 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580856/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580856 Building REAL300025580857 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580857' /scratch/stefan/7787361/working/building/REAL300025580857 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580857 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580857/0 /scratch/stefan/7787361/working/building/REAL300025580857 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/356 `/scratch/stefan/7787361/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=CC(S(=O)(=O)NCC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580857 none CC(=O)C1=CC=CC(S(=O)(=O)NCC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 201, 171, 171, 171, 171, 132, 132, 132, 132, 92, 32, 32, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 171, 201, 201, 201, 171, 171, 171, 132, 92, 92, 31, 9, 8, 8, 8, 171] 201 rigid atoms, others: [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]) total number of confs: 682 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580857 none CC(=O)C1=CC=CC(S(=O)(=O)NCC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 15, 32, 32, 32, 66, 66, 171, 171, 171, 171, 171, 1, 9, 9, 9, 1, 1, 1, 5, 15, 15, 32, 66, 66, 66, 66, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 39, 24, 28, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 462 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580857 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580857 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580857/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580857 Building REAL300025580858 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580858' /scratch/stefan/7787361/working/building/REAL300025580858 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025580858 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580858/0 /scratch/stefan/7787361/working/building/REAL300025580858 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/357 `/scratch/stefan/7787361/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1=CC=CC=N1) `REAL300025580858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580858 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 43, 43, 113, 124, 201, 201, 201, 201, 201, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 43, 113, 113, 124, 124, 10, 10, 1, 1, 1, 1] 201 rigid atoms, others: [32, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300025580858 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 61, 72, 179, 179, 179, 179, 179, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 13, 60, 60, 72, 72, 1, 1, 10, 10, 10, 10] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 450 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580858 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 8, 1, 1, 1, 1, 1, 1, 1, 62, 179, 179, 179, 179, 179, 201, 201, 201, 201, 201, 61, 22, 22, 8, 8, 179, 179, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 411 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580858 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025580858/1 /scratch/stefan/7787361/working/building/REAL300025580858 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/358 `/scratch/stefan/7787361/working/3D/358' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2=CC=CC=N2)NN=C1) `REAL300025580858.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025580858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580858 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2=CC=CC=N2)NN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 11, 29, 29, 99, 109, 201, 201, 201, 201, 201, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 29, 99, 99, 109, 109, 1, 1, 1, 1, 11, 11] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32]) total number of confs: 561 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580858 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2=CC=CC=N2)NN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 56, 70, 160, 160, 160, 160, 160, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 1, 10, 56, 56, 70, 70, 11, 11, 11, 11, 1, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 424 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580858 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2=CC=CC=N2)NN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 68, 160, 160, 201, 201, 201, 201, 201, 160, 160, 160, 68, 24, 24, 8, 8, 201, 201, 201, 201, 160, 160] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580858 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580858 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025580858/1.* 0: /scratch/stefan/7787361/working/building/REAL300025580858/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580858 Building REAL300025580859 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580859' /scratch/stefan/7787361/working/building/REAL300025580859 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580859 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580859/0 /scratch/stefan/7787361/working/building/REAL300025580859 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/359 `/scratch/stefan/7787361/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=C(CC(=O)NCCC2=NC(=O)O[N-]2)C2=CC=C(C)C=C2O1) `REAL300025580859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580859 none CC(=O)C1=C(CC(=O)NCCC2=NC(=O)O[N-]2)C2=CC=C(C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 176, 40, 40, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 40, 8, 8, 8, 8, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 664 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580859 none CC(=O)C1=C(CC(=O)NCCC2=NC(=O)O[N-]2)C2=CC=C(C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 1, 1, 1, 6, 35, 34, 35, 95, 95, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 6, 6, 34, 95, 95, 95, 95, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [1, 3, 4, 5, 35, 40, 17, 18, 19, 20, 21, 22, 23, 24, 36] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 535 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580859 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580859 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580859/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580859 Building REAL300025580860 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580860' /scratch/stefan/7787361/working/building/REAL300025580860 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580860 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580860/0 /scratch/stefan/7787361/working/building/REAL300025580860 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/360 `/scratch/stefan/7787361/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)OC(C)(C)C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025580860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580860 none CN(C(=O)OC(C)(C)C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 72, 136, 163, 163, 201, 201, 201, 201, 72, 72, 72, 38, 38, 38, 16, 8, 1, 1, 1, 1, 1, 1, 1, 72, 136, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 72, 38, 16, 16, 8, 8] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 575 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580860 none CN(C(=O)OC(C)(C)C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 15, 15, 24, 26, 26, 26, 1, 1, 1, 1, 1, 7, 7, 7, 24, 25, 72, 72, 72, 72, 72, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 7, 24, 24, 25, 25] 201 rigid atoms, others: [1, 37, 38, 9, 10, 11, 12, 13, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580860 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580860 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580860/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580860 Building REAL300025580861 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580861' /scratch/stefan/7787361/working/building/REAL300025580861 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580861 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580861/0 /scratch/stefan/7787361/working/building/REAL300025580861 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/361 `/scratch/stefan/7787361/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2)CC(=O)C1) `REAL300025580861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580861 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2)CC(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 23, 23, 77, 98, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 23, 77, 77, 98, 98, 1, 1, 1, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 547 number of broken/clashed sets: 20 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580861 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2)CC(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 55, 81, 180, 180, 180, 180, 180, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 1, 12, 55, 55, 81, 81, 5, 5, 1, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 495 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580861 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2)CC(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 23, 8, 1, 1, 1, 1, 1, 1, 1, 78, 180, 201, 201, 180, 201, 201, 180, 180, 180, 180, 78, 24, 23, 8, 8, 201, 201, 180, 201, 201, 180, 180, 180, 180] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 636 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580861 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580861 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580861/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580861 Building REAL300025580862 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580862' /scratch/stefan/7787361/working/building/REAL300025580862 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580862 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580862/0 /scratch/stefan/7787361/working/building/REAL300025580862 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/362 `/scratch/stefan/7787361/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC1=CC=CC=C1Cl)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580862 none CC(=CC1=CC=CC=C1Cl)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 59, 159, 161, 201, 201, 185, 201, 201, 201, 59, 59, 19, 8, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 201, 201, 201, 201, 59, 19, 19, 8, 8] 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]) total number of confs: 648 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580862 none CC(=CC1=CC=CC=C1Cl)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 26, 26, 26, 98, 108, 201, 201, 201, 201, 201, 4, 4, 4, 4, 1, 1, 1, 1, 26, 98, 98, 108, 108] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 551 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580862 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580862 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580862/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580862 Building REAL300025580863 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580863' /scratch/stefan/7787361/working/building/REAL300025580863 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580863 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580863/0 /scratch/stefan/7787361/working/building/REAL300025580863 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/363 `/scratch/stefan/7787361/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC1=CC=CC(Cl)=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580863 none CC(=CC1=CC=CC(Cl)=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 124, 127, 201, 201, 201, 201, 201, 201, 53, 53, 19, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 201, 201, 201, 201, 53, 19, 19, 8, 8] 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]) total number of confs: 551 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580863 none CC(=CC1=CC=CC(Cl)=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 29, 100, 109, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 1, 1, 1, 29, 100, 100, 109, 109] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 543 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580863 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580863 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580863/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580863 Building REAL300025580864 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580864' /scratch/stefan/7787361/working/building/REAL300025580864 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580864 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580864/0 /scratch/stefan/7787361/working/building/REAL300025580864 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/364 `/scratch/stefan/7787361/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC1=C(Cl)C=CC=C1Cl)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580864 none CC(=CC1=C(Cl)C=CC=C1Cl)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 96, 197, 201, 201, 201, 201, 201, 201, 201, 201, 96, 96, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 96, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 613 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580864 none CC(=CC1=C(Cl)C=CC=C1Cl)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 65, 101, 201, 201, 201, 201, 201, 2, 2, 2, 2, 1, 1, 1, 13, 65, 65, 101, 101] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 580 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580864 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580864 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580864/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580864 Building REAL300025580865 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580865' /scratch/stefan/7787361/working/building/REAL300025580865 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025580865 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580865/0 /scratch/stefan/7787361/working/building/REAL300025580865 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/365 `/scratch/stefan/7787361/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NC(CC1=CNC=N1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580865 none CC(C)CC(=O)NC(CC1=CNC=N1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 131, 131, 131, 110, 60, 110, 124, 142, 142, 142, 142, 60, 60, 21, 8, 1, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 188, 188, 188, 188, 188, 131, 110, 124, 124, 142, 142, 142, 60, 21, 21, 8, 8] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 956 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580865 none CC(C)CC(=O)NC(CC1=CNC=N1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 11, 6, 1, 1, 1, 1, 1, 1, 11, 18, 18, 18, 58, 63, 142, 142, 142, 142, 142, 43, 43, 43, 43, 43, 43, 43, 43, 43, 18, 11, 6, 6, 1, 1, 1, 18, 58, 58, 63, 63] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580865 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025580865/1 /scratch/stefan/7787361/working/building/REAL300025580865 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/366 `/scratch/stefan/7787361/working/3D/366' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NC(CC1=CN=CN1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580865.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025580865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580865 none CC(C)CC(=O)NC(CC1=CN=CN1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 125, 125, 125, 97, 37, 95, 118, 123, 123, 123, 123, 37, 37, 8, 8, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 184, 184, 184, 184, 125, 97, 118, 118, 123, 123, 123, 36, 8, 8, 8, 8] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 921 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580865 none CC(C)CC(=O)NC(CC1=CN=CN1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 39, 14, 14, 14, 8, 4, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 52, 52, 123, 123, 123, 123, 123, 39, 39, 39, 39, 39, 39, 39, 36, 36, 14, 8, 4, 4, 1, 1, 1, 20, 52, 52, 52, 52] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45]) total number of confs: 444 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580865 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580865 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025580865/1.* 0: /scratch/stefan/7787361/working/building/REAL300025580865/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580865 Building REAL300025580866 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580866' /scratch/stefan/7787361/working/building/REAL300025580866 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580866 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580866/0 /scratch/stefan/7787361/working/building/REAL300025580866 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/367 `/scratch/stefan/7787361/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(Cl)=C2)CC(=O)C1) `REAL300025580866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580866 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(Cl)=C2)CC(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 8, 26, 26, 83, 89, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 83, 83, 89, 89, 1, 1, 1, 1, 8, 8, 8, 8] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 505 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580866 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(Cl)=C2)CC(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 38, 46, 133, 133, 133, 133, 133, 1, 1, 8, 8, 7, 8, 8, 8, 1, 1, 1, 1, 9, 38, 38, 46, 46, 8, 8, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 312 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580866 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(Cl)=C2)CC(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 51, 133, 201, 201, 201, 201, 201, 201, 133, 133, 133, 133, 51, 19, 19, 8, 8, 201, 201, 201, 201, 133, 133, 133, 133] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 541 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580866 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580866 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580866/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580866 Building REAL300025580867 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580867' /scratch/stefan/7787361/working/building/REAL300025580867 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580867 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580867/0 /scratch/stefan/7787361/working/building/REAL300025580867 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/368 `/scratch/stefan/7787361/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2)CCC(=O)NC1) `REAL300025580867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580867 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2)CCC(=O)NC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 18, 18, 72, 93, 168, 168, 168, 168, 168, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 18, 72, 72, 93, 93, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] 168 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 29, 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, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 495 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580867 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2)CCC(=O)NC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 34, 53, 165, 165, 165, 165, 165, 1, 1, 7, 7, 2, 7, 7, 1, 1, 1, 1, 1, 1, 6, 34, 34, 53, 53, 7, 7, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1] 168 rigid atoms, others: [1, 34, 35, 36, 37, 38, 39, 40, 11, 12, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 384 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580867 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2)CCC(=O)NC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 23, 8, 1, 1, 1, 1, 1, 1, 1, 82, 165, 168, 168, 168, 168, 168, 165, 165, 165, 165, 165, 165, 82, 24, 24, 8, 8, 168, 168, 168, 168, 168, 165, 165, 165, 165, 165, 165, 165] 168 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 520 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580867 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580867 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580867/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580867 Building REAL300025580868 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580868' /scratch/stefan/7787361/working/building/REAL300025580868 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580868 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580868/0 /scratch/stefan/7787361/working/building/REAL300025580868 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/369 `/scratch/stefan/7787361/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=CO1) `REAL300025580868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580868 none COC(=O)CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 138, 201, 76, 76, 32, 33, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 201, 201, 201, 138, 138, 32, 9, 8, 8, 8, 76, 76, 76, 76] 201 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]) total number of confs: 674 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580868 none COC(=O)CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 6, 29, 1, 1, 1, 1, 7, 7, 7, 23, 23, 76, 76, 76, 76, 76, 1, 1, 1, 1, 30, 30, 30, 6, 6, 7, 23, 23, 23, 23, 2, 2, 2, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 18, 19, 20, 21] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580868 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580868 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580868/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580868 Building REAL300025580869 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580869' /scratch/stefan/7787361/working/building/REAL300025580869 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580869 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580869/0 /scratch/stefan/7787361/working/building/REAL300025580869 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/370 `/scratch/stefan/7787361/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(C(F)(F)F)=C1) `REAL300025580869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580869 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 41, 66, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 7, 41, 41, 66, 66, 1, 1, 1] 151 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 410 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580869 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 22, 8, 1, 1, 1, 1, 1, 1, 1, 71, 151, 151, 151, 151, 151, 151, 151, 151, 151, 70, 22, 22, 8, 8, 151, 151, 151] 151 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580869 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580869 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580869/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580869 Building REAL300025580870 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580870' /scratch/stefan/7787361/working/building/REAL300025580870 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580870 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580870/0 /scratch/stefan/7787361/working/building/REAL300025580870 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/371 `/scratch/stefan/7787361/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CN=CC2=CC=CC=C21)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580870 none CC(CC1=CN=CC2=CC=CC=C21)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 60, 158, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 60, 19, 8, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 199, 199, 201, 201, 201, 201, 201, 201, 60, 19, 19, 8, 8] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 858 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580870 none CC(CC1=CN=CC2=CC=CC=C21)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 30, 30, 30, 104, 110, 201, 201, 201, 201, 201, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 30, 104, 104, 110, 110] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 35, 30, 31] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40]) total number of confs: 577 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580870 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580870 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580870/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580870 Building REAL300025580871 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580871' /scratch/stefan/7787361/working/building/REAL300025580871 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580871 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580871/0 /scratch/stefan/7787361/working/building/REAL300025580871 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/372 `/scratch/stefan/7787361/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2N=CN(C3=CC=C(Cl)C=C3)C2=C1) `REAL300025580871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580871 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2N=CN(C3=CC=C(Cl)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 17, 89, 107, 201, 201, 201, 201, 201, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 89, 89, 107, 107, 5, 5, 5, 1, 1, 1, 1, 5] 201 rigid atoms, others: [35, 36, 37, 38, 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, 39]) total number of confs: 563 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580871 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2N=CN(C3=CC=C(Cl)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 45, 188, 188, 188, 188, 188, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 2, 5, 5, 1, 1, 5, 29, 29, 45, 45, 1, 1, 1, 5, 5, 5, 5, 1] 201 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 372 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580871 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2N=CN(C3=CC=C(Cl)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 22, 8, 1, 1, 1, 1, 1, 1, 1, 76, 188, 188, 188, 188, 188, 188, 188, 201, 201, 201, 201, 201, 201, 188, 188, 76, 22, 22, 8, 8, 188, 188, 188, 201, 201, 201, 201, 188] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 424 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580871 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580871 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580871/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580871 Building REAL300025580872 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580872' /scratch/stefan/7787361/working/building/REAL300025580872 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580872 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580872/0 /scratch/stefan/7787361/working/building/REAL300025580872 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/373 `/scratch/stefan/7787361/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=NC=C1Br) `REAL300025580872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580872 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=NC=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 8, 1, 1, 17, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 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: [7, 1, 7, 7, 41, 57, 158, 158, 158, 158, 158, 1, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 57, 57, 1, 1] 158 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580872 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=NC=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 8, 1, 1, 17, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 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: [80, 80, 20, 8, 1, 1, 1, 1, 1, 1, 1, 80, 158, 158, 158, 158, 158, 158, 158, 80, 21, 21, 8, 8, 158, 158] 158 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580872 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580872 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580872/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580872 Building REAL300025580873 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580873' /scratch/stefan/7787361/working/building/REAL300025580873 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580873 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580873/0 /scratch/stefan/7787361/working/building/REAL300025580873 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/374 `/scratch/stefan/7787361/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025580873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580873 none COC(C)(C)C1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 113, 201, 201, 113, 113, 113, 113, 59, 59, 59, 19, 8, 1, 1, 1, 1, 1, 1, 1, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 113, 113, 58, 19, 19, 8, 8] 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]) total number of confs: 763 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580873 none COC(C)(C)C1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 44, 48, 113, 113, 113, 113, 113, 1, 12, 12, 12, 7, 7, 7, 8, 8, 8, 2, 2, 2, 9, 44, 44, 48, 48] 201 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 21] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580873 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580873 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580873/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580873 Building REAL300025580874 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580874' /scratch/stefan/7787361/working/building/REAL300025580874 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580874 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580874/0 /scratch/stefan/7787361/working/building/REAL300025580874 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/375 `/scratch/stefan/7787361/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(F)(F)F)=NN1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580874 none CC1=CC(C(F)(F)F)=NN1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 15, 15, 15, 8, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 50, 50, 50, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 167, 167, 50, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 683 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580874 none CC1=CC(C(F)(F)F)=NN1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 15, 15, 15, 8, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 4, 30, 30, 30, 97, 104, 201, 201, 201, 201, 201, 2, 2, 2, 1, 4, 4, 30, 97, 97, 104, 104] 201 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 25] set([5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 584 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580874 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580874 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580874/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580874 Building REAL300025580875 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580875' /scratch/stefan/7787361/working/building/REAL300025580875 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580875 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580875/0 /scratch/stefan/7787361/working/building/REAL300025580875 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/376 `/scratch/stefan/7787361/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C(C(F)(F)F)=NN1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580875 none CC1=C(Cl)C(C(F)(F)F)=NN1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 5, 15, 15, 15, 8, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 45, 45, 45, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 149, 149, 45, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 656 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580875 none CC1=C(Cl)C(C(F)(F)F)=NN1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 5, 15, 15, 15, 8, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 6, 30, 30, 30, 106, 107, 201, 201, 201, 201, 201, 2, 2, 2, 6, 6, 30, 106, 106, 107, 107] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 11] set([6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580875 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580875 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580875/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580875 Building REAL300025580876 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580876' /scratch/stefan/7787361/working/building/REAL300025580876 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580876 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580876/0 /scratch/stefan/7787361/working/building/REAL300025580876 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/377 `/scratch/stefan/7787361/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC(Br)=C1) `REAL300025580876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580876 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 32, 32, 111, 112, 201, 201, 201, 201, 201, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 32, 111, 111, 112, 112, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 544 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580876 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 61, 62, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 1, 6, 6, 3, 6, 6, 6, 13, 61, 61, 62, 62, 1, 1, 6, 6, 6, 6] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 351 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580876 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 46, 145, 145, 145, 145, 145, 201, 201, 201, 201, 201, 201, 46, 19, 19, 8, 8, 145, 145, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 538 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580876 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580876 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580876/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580876 Building REAL300025580877 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580877' /scratch/stefan/7787361/working/building/REAL300025580877 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580877 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580877/0 /scratch/stefan/7787361/working/building/REAL300025580877 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/378 `/scratch/stefan/7787361/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1) `REAL300025580877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580877 none CC(C)(C)OC(=O)NCCCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 136, 200, 39, 37, 37, 36, 17, 17, 17, 9, 9, 9, 7, 5, 1, 1, 1, 1, 1, 1, 1, 17, 17, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 39, 39, 37, 37, 37, 37, 36, 36, 17, 9, 7, 7, 5, 5] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 642 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580877 none CC(C)(C)OC(=O)NCCCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 64, 38, 64, 9, 7, 7, 6, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 17, 17, 17, 17, 17, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 38, 9, 9, 7, 7, 7, 7, 6, 6, 1, 4, 9, 9, 9, 9] 201 rigid atoms, others: [11, 12, 13, 46, 15, 14, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580877 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580877 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580877/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580877 Building REAL300025580878 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580878' /scratch/stefan/7787361/working/building/REAL300025580878 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580878 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580878/0 /scratch/stefan/7787361/working/building/REAL300025580878 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/379 `/scratch/stefan/7787361/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1) `REAL300025580878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580878 none CS(=O)(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 48, 53, 53, 43, 43, 43, 17, 8, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 53, 53, 53, 43, 17, 17, 8, 8, 48, 48, 48, 48, 48, 48, 48, 48] 53 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 200 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580878 none CS(=O)(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 1, 1, 8, 8, 8, 23, 23, 48, 48, 48, 48, 48, 1, 1, 1, 1, 7, 7, 7, 8, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1] 53 rigid atoms, others: [32, 1, 34, 35, 4, 5, 33, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 139 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580878 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580878 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580878/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580878 Building REAL300025580879 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580879' /scratch/stefan/7787361/working/building/REAL300025580879 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580879 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580879/0 /scratch/stefan/7787361/working/building/REAL300025580879 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/380 `/scratch/stefan/7787361/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(N2C=CN=N2)C=CS1) `REAL300025580879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580879 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(N2C=CN=N2)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 8, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 18, 18, 68, 87, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 68, 68, 87, 87, 1, 1, 7, 7] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 535 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580879 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(N2C=CN=N2)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 8, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 47, 69, 181, 181, 181, 181, 181, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 10, 47, 47, 69, 69, 7, 7, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 18, 19, 20, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 455 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580879 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(N2C=CN=N2)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 8, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 68, 181, 181, 201, 201, 201, 201, 181, 181, 181, 68, 23, 23, 8, 8, 201, 201, 181, 181] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 426 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580879 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580879 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580879/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580879 Building REAL300025580880 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580880' /scratch/stefan/7787361/working/building/REAL300025580880 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580880 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580880/0 /scratch/stefan/7787361/working/building/REAL300025580880 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/381 `/scratch/stefan/7787361/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C2=NC=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)OCCO1) `REAL300025580880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580880 none CC1(C2=NC=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)OCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 12, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 101, 101, 101, 101, 64, 64, 64, 21, 8, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 201, 201, 201, 101, 64, 21, 21, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 568 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580880 none CC1(C2=NC=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)OCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 12, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 1, 1, 1, 1, 1, 6, 6, 6, 33, 41, 101, 101, 101, 101, 101, 1, 13, 13, 13, 13, 13, 13, 13, 1, 6, 33, 33, 41, 41, 13, 13, 13, 13] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580880 none CC1(C2=NC=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)OCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 12, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 13, 13, 13, 13, 44, 43, 44, 117, 137, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 2, 2, 2, 13, 44, 117, 117, 137, 137, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 33, 32, 34, 18, 19, 20, 21, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580880 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580880 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580880/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580880 Building REAL300025580881 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580881' /scratch/stefan/7787361/working/building/REAL300025580881 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580881 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580881/0 /scratch/stefan/7787361/working/building/REAL300025580881 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/382 `/scratch/stefan/7787361/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CN(C(=O)C2CCCCC2)C1) `REAL300025580881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580881 none O=C(NCCC1=NC(=O)O[N-]1)C1CN(C(=O)C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 43, 43, 117, 117, 201, 201, 201, 201, 201, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 43, 117, 117, 117, 117, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 31] 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, 42, 43]) total number of confs: 585 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580881 none O=C(NCCC1=NC(=O)O[N-]1)C1CN(C(=O)C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 41, 42, 108, 108, 108, 108, 108, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 1, 9, 41, 41, 42, 42, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1] 201 rigid atoms, others: [1, 43, 42, 11, 12, 13, 14, 22, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580881 none O=C(NCCC1=NC(=O)O[N-]1)C1CN(C(=O)C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 1, 1, 1, 1, 1, 1, 1, 45, 108, 108, 108, 140, 140, 201, 201, 201, 201, 201, 108, 45, 15, 15, 7, 7, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 108] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 711 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580881 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580881 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580881/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580881 Building REAL300025580882 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580882' /scratch/stefan/7787361/working/building/REAL300025580882 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580882 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580882/0 /scratch/stefan/7787361/working/building/REAL300025580882 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/383 `/scratch/stefan/7787361/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580882 none COC1=CC=CC([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 165, 165, 165, 165, 165, 134, 134, 134, 134, 40, 134, 40, 40, 16, 8, 1, 1, 1, 1, 1, 1, 1, 165, 201, 201, 201, 165, 165, 165, 134, 134, 40, 16, 16, 8, 8, 165] 201 rigid atoms, others: [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: 520 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580882 none COC1=CC=CC([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 57, 57, 134, 134, 134, 134, 134, 4, 6, 6, 6, 4, 4, 4, 1, 1, 12, 57, 57, 57, 57, 4] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 316 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580882 none COC1=CC=CC([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 24, 24, 24, 88, 88, 165, 165, 165, 165, 165, 1, 2, 2, 2, 1, 1, 1, 4, 4, 24, 88, 88, 88, 88, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 23, 27, 28, 29, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 444 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580882 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580882 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580882/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580882 Building REAL300025580883 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580883' /scratch/stefan/7787361/working/building/REAL300025580883 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580883 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580883/0 /scratch/stefan/7787361/working/building/REAL300025580883 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/384 `/scratch/stefan/7787361/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC1=CC(I)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580883 none CNC1=CC(I)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 18, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 174, 201, 201, 201, 75, 75, 75, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 74, 23, 23, 8, 8] 201 rigid atoms, others: [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: 549 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580883 none CNC1=CC(I)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 18, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 59, 89, 201, 201, 201, 201, 201, 7, 7, 7, 7, 1, 1, 1, 12, 59, 59, 89, 89] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 564 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580883 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580883 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580883/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580883 Building REAL300025580884 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580884' /scratch/stefan/7787361/working/building/REAL300025580884 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580884 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580884/0 /scratch/stefan/7787361/working/building/REAL300025580884 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/385 `/scratch/stefan/7787361/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(I)C=N1) `REAL300025580884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580884 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(I)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 18, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [13, 1, 13, 13, 53, 63, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 1, 13, 53, 53, 63, 63, 1, 1, 1] 112 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580884 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(I)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 18, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [75, 75, 22, 8, 1, 1, 1, 1, 1, 1, 1, 75, 112, 112, 112, 112, 112, 112, 75, 22, 22, 8, 8, 112, 112, 112] 112 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580884 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580884 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580884/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580884 Building REAL300025580885 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580885' /scratch/stefan/7787361/working/building/REAL300025580885 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580885 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580885/0 /scratch/stefan/7787361/working/building/REAL300025580885 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/386 `/scratch/stefan/7787361/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1)C(F)(F)F) `REAL300025580885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580885 none CC(C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 173, 173, 173, 173, 78, 78, 79, 22, 8, 1, 1, 1, 1, 1, 1, 1, 173, 173, 200, 200, 200, 200, 200, 200, 200, 200, 173, 173, 78, 22, 22, 8, 8, 173, 173] 200 rigid atoms, others: [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]) total number of confs: 554 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580885 none CC(C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 32, 57, 173, 173, 173, 173, 173, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 6, 32, 32, 57, 57, 1, 1] 200 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 17, 18, 35, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580885 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580885 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580885/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580885 Building REAL300025580886 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580886' /scratch/stefan/7787361/working/building/REAL300025580886 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580886 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580886/0 /scratch/stefan/7787361/working/building/REAL300025580886 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/387 `/scratch/stefan/7787361/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OC2=CC=CC=C2CC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580886 none CC1=CC=C(OC2=CC=CC=C2CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 157, 157, 157, 127, 157, 157, 94, 27, 27, 27, 13, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 157, 157, 157, 157, 94, 94, 27, 13, 13, 7, 7, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 669 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580886 none CC1=CC=C(OC2=CC=CC=C2CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 25, 25, 25, 83, 85, 157, 157, 157, 157, 157, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 25, 83, 83, 85, 85, 4, 4] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 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: 467 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580886 none CC1=CC=C(OC2=CC=CC=C2CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 11, 39, 39, 39, 107, 109, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4, 11, 11, 39, 107, 107, 109, 109, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 43, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 616 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580886 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580886 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580886/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580886 Building REAL300025580887 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580887' /scratch/stefan/7787361/working/building/REAL300025580887 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580887 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580887/0 /scratch/stefan/7787361/working/building/REAL300025580887 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/388 `/scratch/stefan/7787361/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(S(=O)(=O)CC2CC2)C=C1) `REAL300025580887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580887 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(S(=O)(=O)CC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 47, 47, 117, 120, 201, 201, 201, 201, 201, 29, 29, 29, 17, 5, 17, 17, 1, 1, 1, 1, 29, 29, 47, 117, 117, 120, 120, 29, 29, 5, 5, 1, 1, 1, 1, 1, 29, 29] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38, 39]) total number of confs: 639 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580887 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(S(=O)(=O)CC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 17, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 1, 1, 3, 15, 15, 17, 17, 1, 1, 14, 14, 29, 29, 29, 29, 29, 1, 1] 201 rigid atoms, others: [1, 38, 39, 11, 12, 13, 14, 15, 22, 23, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580887 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(S(=O)(=O)CC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 1, 1, 1, 1, 1, 1, 1, 41, 66, 66, 66, 66, 97, 97, 97, 157, 201, 201, 66, 66, 41, 16, 16, 8, 8, 66, 66, 157, 157, 201, 201, 201, 201, 201, 66, 66] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 865 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580887 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580887 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580887/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580887 Building REAL300025580888 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580888' /scratch/stefan/7787361/working/building/REAL300025580888 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580888 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580888/0 /scratch/stefan/7787361/working/building/REAL300025580888 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/389 `/scratch/stefan/7787361/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC1=CC=C(C#N)C=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580888 none CC(C)(CC1=CC=C(C#N)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 59, 145, 145, 201, 201, 201, 201, 201, 201, 201, 201, 59, 59, 17, 8, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 145, 145, 201, 201, 201, 201, 201, 201, 59, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 882 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580888 none CC(C)(CC1=CC=C(C#N)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 20, 20, 20, 94, 105, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 20, 94, 94, 105, 105] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 12, 13, 14, 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: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580888 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580888 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580888/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580888 Building REAL300025580889 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580889' /scratch/stefan/7787361/working/building/REAL300025580889 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580889 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580889/0 /scratch/stefan/7787361/working/building/REAL300025580889 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/390 `/scratch/stefan/7787361/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C([N+](=O)[O-])=C1) `REAL300025580889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580889 none CS(=O)(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [146, 90, 146, 146, 90, 140, 140, 90, 90, 90, 23, 8, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 146, 146, 146, 140, 140, 90, 23, 23, 8, 8, 140] 160 rigid atoms, others: [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: 810 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580889 none CS(=O)(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 28, 45, 140, 140, 140, 140, 140, 1, 1, 2, 2, 1, 3, 3, 3, 1, 1, 5, 28, 28, 45, 45, 1] 160 rigid atoms, others: [1, 34, 4, 5, 6, 7, 8, 19, 20, 23, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580889 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580889 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580889/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580889 Building REAL300025580890 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580890' /scratch/stefan/7787361/working/building/REAL300025580890 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580890 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580890/0 /scratch/stefan/7787361/working/building/REAL300025580890 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/391 `/scratch/stefan/7787361/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC([N+](=O)[O-])=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl) `REAL300025580890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580890 none CC1=CC([N+](=O)[O-])=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 95, 95, 95, 95, 83, 83, 83, 23, 8, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 95, 83, 23, 23, 8, 8, 95] 95 rigid atoms, others: [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: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580890 none CC1=CC([N+](=O)[O-])=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 23, 38, 95, 95, 95, 95, 95, 1, 1, 1, 2, 2, 2, 1, 7, 23, 23, 38, 38, 1] 95 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 19, 20, 21, 25, 31] set([5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580890 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580890 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580890/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580890 Building REAL300025580891 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580891' /scratch/stefan/7787361/working/building/REAL300025580891 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580891 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580891/0 /scratch/stefan/7787361/working/building/REAL300025580891 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/392 `/scratch/stefan/7787361/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC=C1C(F)(F)F) `REAL300025580891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580891 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 21, 21, 71, 88, 201, 201, 201, 201, 201, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 71, 71, 88, 88, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 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]) total number of confs: 540 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580891 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 52, 69, 169, 169, 169, 169, 169, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 52, 52, 69, 69, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 434 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580891 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 9, 1, 1, 1, 1, 1, 1, 1, 59, 169, 169, 169, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 59, 22, 22, 9, 9, 169, 169, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 539 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580891 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580891 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580891/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580891 Building REAL300025580892 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580892' /scratch/stefan/7787361/working/building/REAL300025580892 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580892 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580892/0 /scratch/stefan/7787361/working/building/REAL300025580892 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/393 `/scratch/stefan/7787361/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(C(F)(F)F)C=C1) `REAL300025580892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580892 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 37, 37, 103, 114, 201, 201, 201, 201, 201, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 37, 103, 103, 114, 114, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 572 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580892 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 67, 83, 174, 174, 174, 174, 174, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 5, 5, 13, 67, 67, 83, 83, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 485 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580892 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 69, 174, 174, 174, 174, 174, 201, 201, 174, 185, 201, 201, 201, 201, 201, 68, 23, 23, 8, 8, 174, 174, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 782 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580892 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580892 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580892/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580892 Building REAL300025580893 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580893' /scratch/stefan/7787361/working/building/REAL300025580893 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580893 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580893/0 /scratch/stefan/7787361/working/building/REAL300025580893 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/394 `/scratch/stefan/7787361/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCC1=CC=CC(Cl)=C1)NCCC1=NC(=O)O[N-]1) `REAL300025580893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580893 none O=C(COCC1=CC=CC(Cl)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 1, 1, 16, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 54, 70, 114, 201, 201, 199, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 62, 62, 114, 114, 201, 201, 201, 201, 28, 7, 7, 7, 7] 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]) total number of confs: 596 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580893 none O=C(COCC1=CC=CC(Cl)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 1, 1, 16, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 55, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 119, 119, 201, 201, 201, 201, 201, 55, 55, 8, 8, 1, 1, 1, 1, 62, 119, 119, 119, 119] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 672 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580893 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580893 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580893/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580893 Building REAL300025580894 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580894' /scratch/stefan/7787361/working/building/REAL300025580894 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580894 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580894/0 /scratch/stefan/7787361/working/building/REAL300025580894 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/395 `/scratch/stefan/7787361/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)C=C1) `REAL300025580894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580894 none CC1=CC=C(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 201, 201, 197, 67, 67, 67, 67, 51, 51, 51, 20, 8, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 67, 67, 51, 20, 21, 8, 8, 67, 201, 201] 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]) total number of confs: 409 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580894 none CC1=CC=C(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 13, 13, 9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 18, 24, 67, 67, 67, 67, 67, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 4, 18, 18, 24, 24, 1, 13, 13] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 21, 22, 37, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580894 none CC1=CC=C(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 22, 22, 22, 87, 102, 201, 201, 201, 201, 201, 13, 13, 1, 1, 2, 2, 2, 1, 1, 13, 13, 22, 87, 87, 102, 102, 13, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 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 /scratch/stefan/7787361/working/building/REAL300025580894 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580894 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580894/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580894 Building REAL300025580895 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580895' /scratch/stefan/7787361/working/building/REAL300025580895 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580895 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580895/0 /scratch/stefan/7787361/working/building/REAL300025580895 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/396 `/scratch/stefan/7787361/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CO1) `REAL300025580895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580895 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 12, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 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: [12, 1, 12, 12, 54, 80, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 12, 54, 54, 80, 80, 1, 1] 131 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) total number of confs: 414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580895 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 12, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 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: [78, 78, 23, 8, 1, 1, 1, 1, 1, 1, 1, 78, 131, 131, 131, 131, 130, 77, 23, 23, 8, 8, 131, 130] 131 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580895 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580895 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580895/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580895 Building REAL300025580896 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580896' /scratch/stefan/7787361/working/building/REAL300025580896 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580896 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580896/0 /scratch/stefan/7787361/working/building/REAL300025580896 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/397 `/scratch/stefan/7787361/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(OCC2=CC=CC=C2)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025580896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580896 none CC1=CC(OCC2=CC=CC=C2)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 131, 201, 201, 201, 201, 201, 201, 42, 42, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 201, 201, 201, 201, 201, 201, 201, 41, 8, 8, 8, 8] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 565 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580896 none CC1=CC(OCC2=CC=CC=C2)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 17, 3, 1, 1, 1, 1, 1, 1, 1, 52, 52, 66, 66, 66, 114, 114, 201, 201, 201, 201, 201, 52, 52, 52, 52, 52, 3, 3, 1, 1, 1, 1, 1, 66, 114, 114, 114, 114] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40]) total number of confs: 528 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580896 none CC1=CC(OCC2=CC=CC=C2)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 28, 52, 52, 33, 52, 52, 1, 1, 7, 7, 7, 25, 25, 90, 90, 90, 90, 90, 1, 2, 2, 2, 1, 28, 28, 52, 52, 52, 52, 52, 7, 25, 25, 25, 25] 201 rigid atoms, others: [0, 1, 2, 3, 4, 12, 13, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580896 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580896 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580896/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580896 Building REAL300025580897 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580897' /scratch/stefan/7787361/working/building/REAL300025580897 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580897 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580897/0 /scratch/stefan/7787361/working/building/REAL300025580897 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/398 `/scratch/stefan/7787361/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=CC(F)=C2)C=N1) `REAL300025580897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580897 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=CC(F)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 19, 32, 32, 94, 109, 201, 201, 201, 201, 201, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 32, 94, 94, 109, 109, 19, 19, 1, 1, 1, 1, 19] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 592 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580897 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=CC(F)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 14, 18, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1, 4, 14, 14, 18, 18, 1, 1, 19, 19, 19, 19, 1] 201 rigid atoms, others: [1, 36, 11, 12, 13, 14, 15, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580897 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=CC(F)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 11, 7, 1, 1, 1, 1, 1, 1, 1, 31, 37, 37, 37, 37, 128, 201, 201, 201, 201, 201, 201, 37, 37, 31, 11, 11, 7, 7, 37, 37, 201, 201, 201, 201, 37] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580897 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580897 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580897/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580897 Building REAL300025580898 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580898' /scratch/stefan/7787361/working/building/REAL300025580898 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580898 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580898/0 /scratch/stefan/7787361/working/building/REAL300025580898 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/399 `/scratch/stefan/7787361/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1) `REAL300025580898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580898 none CC1=CC=CC=C1OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 201, 201, 166, 58, 58, 58, 58, 46, 46, 46, 18, 8, 1, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 201, 186, 201, 201, 58, 58, 46, 19, 19, 8, 8, 58] 201 rigid atoms, others: [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]) total number of confs: 452 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580898 none CC1=CC=CC=C1OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 19, 19, 9, 1, 1, 1, 1, 1, 1, 3, 3, 4, 17, 21, 58, 58, 58, 58, 58, 1, 1, 19, 19, 19, 19, 15, 19, 19, 1, 1, 4, 17, 17, 21, 21, 1] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580898 none CC1=CC=CC=C1OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 27, 27, 27, 83, 97, 201, 201, 201, 201, 201, 19, 19, 2, 2, 2, 1, 1, 1, 1, 19, 19, 27, 83, 83, 97, 97, 19] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 560 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580898 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580898 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580898/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580898 Building REAL300025580899 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580899' /scratch/stefan/7787361/working/building/REAL300025580899 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580899 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580899/0 /scratch/stefan/7787361/working/building/REAL300025580899 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/400 `/scratch/stefan/7787361/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CC=C1OC1CCCC1)NCCC1=NC(=O)O[N-]1) `REAL300025580899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580899 none O=C(CC1=CC=CC=C1OC1CCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 96, 124, 124, 124, 124, 124, 124, 189, 201, 201, 201, 201, 11, 7, 1, 1, 1, 1, 1, 1, 1, 96, 96, 124, 124, 124, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 24, 11, 11, 7, 7] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 559 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580899 none O=C(CC1=CC=CC=C1OC1CCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 31, 16, 16, 16, 6, 16, 16, 6, 1, 1, 1, 1, 1, 1, 68, 68, 124, 124, 201, 201, 201, 201, 201, 31, 31, 16, 10, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 124, 124, 124, 124] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 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, 29, 39, 40, 41, 42, 43]) total number of confs: 678 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580899 none O=C(CC1=CC=CC=C1OC1CCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 23, 23, 62, 62, 124, 124, 124, 124, 124, 5, 5, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 62, 62, 62, 62] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 387 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580899 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580899 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580899/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580899 Building REAL300025580900 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580900' /scratch/stefan/7787361/working/building/REAL300025580900 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580900 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580900/0 /scratch/stefan/7787361/working/building/REAL300025580900 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/401 `/scratch/stefan/7787361/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=CC(Cl)=C2)C=N1) `REAL300025580900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580900 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=CC(Cl)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 25, 38, 38, 101, 113, 201, 201, 201, 201, 201, 24, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 38, 101, 101, 113, 113, 25, 25, 1, 1, 1, 1, 25] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 594 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580900 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=CC(Cl)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 14, 18, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 9, 25, 25, 25, 25, 25, 25, 1, 1, 4, 14, 14, 18, 18, 1, 1, 25, 25, 25, 25, 1] 201 rigid atoms, others: [1, 36, 11, 12, 13, 14, 15, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580900 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=CC(Cl)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 11, 7, 1, 1, 1, 1, 1, 1, 1, 30, 36, 36, 36, 36, 122, 201, 201, 201, 201, 201, 201, 36, 36, 30, 12, 12, 7, 7, 36, 36, 201, 201, 201, 201, 36] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580900 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580900 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580900/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580900 Building REAL300025580901 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580901' /scratch/stefan/7787361/working/building/REAL300025580901 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580901 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580901/0 /scratch/stefan/7787361/working/building/REAL300025580901 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/402 `/scratch/stefan/7787361/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)=C1) `REAL300025580901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580901 none CC1=CC=CC(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 192, 201, 201, 117, 39, 39, 39, 39, 29, 29, 29, 11, 7, 1, 1, 1, 1, 1, 1, 1, 39, 39, 201, 201, 201, 201, 195, 201, 201, 39, 39, 29, 12, 12, 7, 7, 39, 201] 201 rigid atoms, others: [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]) total number of confs: 409 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580901 none CC1=CC=CC(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 23, 9, 1, 1, 1, 1, 1, 1, 3, 3, 4, 15, 19, 39, 39, 39, 39, 39, 1, 1, 23, 23, 23, 23, 19, 23, 23, 1, 1, 4, 15, 15, 19, 19, 1, 23] 201 rigid atoms, others: [32, 38, 6, 7, 8, 9, 10, 11, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 39]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580901 none CC1=CC=CC(OC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 37, 37, 37, 103, 118, 201, 201, 201, 201, 201, 23, 22, 1, 2, 2, 2, 1, 1, 1, 23, 23, 37, 103, 103, 118, 118, 23, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 24, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 608 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580901 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580901 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580901/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580901 Building REAL300025580902 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580902' /scratch/stefan/7787361/working/building/REAL300025580902 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580902 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580902/0 /scratch/stefan/7787361/working/building/REAL300025580902 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/403 `/scratch/stefan/7787361/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1OCCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580902 none CC(C)(C)OC(=O)NCC1OCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 17, 23, 13, 11, 11, 11, 11, 11, 11, 11, 11, 9, 7, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 17, 13, 13, 11, 11, 11, 11, 11, 11, 11, 9, 9, 7, 7] 23 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580902 none CC(C)(C)OC(=O)NCC1OCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 8, 10, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 5, 5, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6] 23 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] 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, 34, 35, 36, 43, 44, 45, 46, 47]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580902 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580902 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580902/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580902 Building REAL300025580903 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580903' /scratch/stefan/7787361/working/building/REAL300025580903 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580903 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580903/0 /scratch/stefan/7787361/working/building/REAL300025580903 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/404 `/scratch/stefan/7787361/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(C(=O)OC(C)(C)C)=C1) `REAL300025580903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580903 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(C(=O)OC(C)(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 17, 8, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 201, 201, 201, 201, 201, 201, 97, 97, 97, 97, 97, 35, 17, 17, 8, 8, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 538 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580903 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(C(=O)OC(C)(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 29, 33, 97, 97, 97, 97, 97, 1, 1, 1, 10, 10, 12, 12, 12, 12, 1, 2, 2, 2, 1, 5, 29, 29, 33, 33, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 34, 15, 16, 17, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580903 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580903 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580903/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580903 Building REAL300025580904 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580904' /scratch/stefan/7787361/working/building/REAL300025580904 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580904 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580904/0 /scratch/stefan/7787361/working/building/REAL300025580904 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/405 `/scratch/stefan/7787361/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(Br)C=C1) `REAL300025580904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580904 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 30, 30, 106, 114, 201, 201, 201, 201, 201, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 30, 106, 106, 114, 114, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 560 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580904 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 54, 62, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 12, 54, 54, 62, 62, 1, 1, 4, 4, 4, 4] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 350 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580904 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 9, 1, 1, 1, 1, 1, 1, 1, 55, 134, 135, 135, 135, 135, 201, 201, 135, 135, 201, 201, 55, 19, 19, 8, 8, 135, 135, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 693 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580904 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580904 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580904/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580904 Building REAL300025580905 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580905' /scratch/stefan/7787361/working/building/REAL300025580905 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580905 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580905/0 /scratch/stefan/7787361/working/building/REAL300025580905 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/406 `/scratch/stefan/7787361/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025580905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580905 none CC1=CC(Br)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 177, 177, 76, 76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 76, 24, 24, 8, 8] 177 rigid atoms, others: [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]) total number of confs: 399 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580905 none CC1=CC(Br)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 41, 65, 177, 177, 177, 177, 177, 1, 2, 2, 2, 1, 7, 41, 41, 65, 65] 177 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 21] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580905 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580905 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580905/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580905 Building REAL300025580906 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580906' /scratch/stefan/7787361/working/building/REAL300025580906 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580906 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580906/0 /scratch/stefan/7787361/working/building/REAL300025580906 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/407 `/scratch/stefan/7787361/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(CCC(=O)NCCC2=NC(=O)O[N-]2)OC=N1) `REAL300025580906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580906 none COC(=O)C1=C(CCC(=O)NCCC2=NC(=O)O[N-]2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 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, 48, 72, 48, 42, 42, 32, 32, 32, 14, 7, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 72, 72, 72, 42, 42, 42, 42, 32, 14, 14, 7, 7, 48] 72 rigid atoms, others: [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: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580906 none COC(=O)C1=C(CCC(=O)NCCC2=NC(=O)O[N-]2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 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: [6, 6, 1, 6, 1, 1, 1, 4, 5, 5, 5, 5, 17, 21, 48, 48, 48, 48, 48, 1, 1, 1, 7, 7, 7, 4, 4, 5, 5, 5, 17, 17, 21, 21, 1] 72 rigid atoms, others: [2, 4, 5, 6, 34, 19, 20, 21] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580906 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580906 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580906/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580906 Building REAL300025580907 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580907' /scratch/stefan/7787361/working/building/REAL300025580907 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580907 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580907/0 /scratch/stefan/7787361/working/building/REAL300025580907 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/408 `/scratch/stefan/7787361/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)N=C2CCCCN21) `REAL300025580907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580907 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)N=C2CCCCN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 8, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 37, 63, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 63, 63, 1, 1, 1, 1, 1, 1, 1, 1] 153 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 407 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580907 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)N=C2CCCCN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 8, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 20, 8, 1, 1, 1, 1, 1, 1, 1, 94, 153, 153, 153, 153, 153, 153, 153, 153, 153, 94, 20, 20, 8, 8, 153, 153, 153, 153, 153, 153, 153, 153] 153 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580907 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580907 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580907/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580907 Building REAL300025580908 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580908' /scratch/stefan/7787361/working/building/REAL300025580908 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580908 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580908/0 /scratch/stefan/7787361/working/building/REAL300025580908 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/409 `/scratch/stefan/7787361/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(S(=O)(=O)C2=CC=C(Cl)C=C2)CC1) `REAL300025580908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580908 none O=C(NCCC1=NC(=O)O[N-]1)C1(S(=O)(=O)C2=CC=C(Cl)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 7, 26, 26, 99, 101, 201, 201, 201, 201, 201, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 99, 99, 101, 101, 1, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 547 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580908 none O=C(NCCC1=NC(=O)O[N-]1)C1(S(=O)(=O)C2=CC=C(Cl)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 34, 38, 124, 124, 124, 124, 124, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 7, 34, 34, 38, 38, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 33, 11, 12, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580908 none O=C(NCCC1=NC(=O)O[N-]1)C1(S(=O)(=O)C2=CC=C(Cl)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 52, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124, 52, 17, 17, 8, 8, 201, 201, 201, 201, 124, 124, 124, 124] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 775 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580908 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580908 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580908/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580908 Building REAL300025580909 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580909' /scratch/stefan/7787361/working/building/REAL300025580909 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580909 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580909/0 /scratch/stefan/7787361/working/building/REAL300025580909 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/410 `/scratch/stefan/7787361/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1)OCC) `REAL300025580909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580909 none CCOC(CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 85, 85, 60, 60, 60, 31, 32, 32, 13, 7, 1, 1, 1, 1, 1, 1, 1, 60, 60, 85, 170, 172, 169, 169, 169, 169, 169, 85, 85, 85, 60, 31, 13, 13, 7, 7, 60, 172, 172, 172, 172, 172] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43]) total number of confs: 589 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580909 none CCOC(CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 16, 7, 5, 1, 1, 1, 1, 1, 5, 5, 5, 21, 25, 60, 60, 60, 60, 60, 1, 1, 7, 16, 19, 19, 19, 19, 19, 19, 7, 5, 5, 1, 5, 21, 21, 25, 25, 1, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 19, 20, 38] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 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 /scratch/stefan/7787361/working/building/REAL300025580909 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580909 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580909/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580909 Building REAL300025580910 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580910' /scratch/stefan/7787361/working/building/REAL300025580910 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580910 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580910/0 /scratch/stefan/7787361/working/building/REAL300025580910 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/411 `/scratch/stefan/7787361/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CN2C=C(C(=O)NCCC3=NC(=O)O[N-]3)N=N2)COC1) `REAL300025580910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580910 none CCC1(CN2C=C(C(=O)NCCC3=NC(=O)O[N-]3)N=N2)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 174, 73, 73, 73, 52, 52, 52, 21, 8, 1, 1, 1, 1, 1, 1, 1, 72, 72, 201, 201, 201, 201, 201, 201, 201, 201, 174, 174, 73, 51, 21, 21, 8, 8, 201, 201, 201, 201] 201 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, 37, 38, 39]) total number of confs: 784 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580910 none CCC1(CN2C=C(C(=O)NCCC3=NC(=O)O[N-]3)N=N2)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 5, 1, 1, 1, 1, 1, 6, 6, 6, 16, 22, 72, 72, 72, 72, 73, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 1, 6, 16, 16, 22, 22, 8, 8, 8, 8] 201 rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 30] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580910 none CCC1(CN2C=C(C(=O)NCCC3=NC(=O)O[N-]3)N=N2)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 4, 8, 8, 8, 32, 32, 32, 72, 87, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 8, 32, 72, 72, 87, 87, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 36, 37, 38, 39, 20, 21, 22] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 537 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580910 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580910 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580910/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580910 Building REAL300025580911 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580911' /scratch/stefan/7787361/working/building/REAL300025580911 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580911 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580911/0 /scratch/stefan/7787361/working/building/REAL300025580911 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/412 `/scratch/stefan/7787361/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC1=CC=C(OC(F)(F)F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580911 none CC(=CC1=CC=C(OC(F)(F)F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 87, 88, 88, 88, 88, 88, 201, 201, 201, 201, 88, 88, 33, 33, 14, 7, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88, 88, 88, 88, 33, 14, 14, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 468 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580911 none CC(=CC1=CC=C(OC(F)(F)F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 12, 19, 19, 20, 1, 1, 2, 10, 10, 10, 32, 32, 88, 88, 88, 88, 88, 2, 2, 2, 2, 1, 1, 1, 1, 10, 32, 32, 32, 32] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 12, 13, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 244 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580911 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580911 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580911/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580911 Building REAL300025580912 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580912' /scratch/stefan/7787361/working/building/REAL300025580912 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580912 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580912/0 /scratch/stefan/7787361/working/building/REAL300025580912 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/413 `/scratch/stefan/7787361/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(C(F)(F)F)=N1) `REAL300025580912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580912 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 5, 15, 15, 15, 8, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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: [12, 1, 12, 12, 63, 83, 165, 165, 165, 165, 165, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 63, 63, 83, 83, 1, 1] 165 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 20, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 471 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580912 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 5, 15, 15, 15, 8, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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: [97, 97, 23, 8, 1, 1, 1, 1, 1, 1, 1, 97, 165, 165, 165, 165, 165, 165, 165, 165, 165, 97, 23, 23, 8, 8, 165, 165] 165 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580912 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580912 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580912/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580912 Building REAL300025580913 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580913' /scratch/stefan/7787361/working/building/REAL300025580913 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580913 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580913/0 /scratch/stefan/7787361/working/building/REAL300025580913 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/414 `/scratch/stefan/7787361/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CC2=CC=C(Cl)C=C2Cl)N=N1) `REAL300025580913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580913 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CC2=CC=C(Cl)C=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 12, 26, 26, 80, 98, 201, 201, 201, 201, 201, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 26, 80, 80, 98, 98, 12, 5, 5, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 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]) total number of confs: 557 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580913 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CC2=CC=C(Cl)C=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 19, 24, 56, 56, 56, 56, 56, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 12, 12, 1, 1, 6, 18, 18, 24, 24, 1, 6, 6, 12, 12, 12] 201 rigid atoms, others: [1, 11, 12, 13, 14, 23, 24, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580913 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CC2=CC=C(Cl)C=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 1, 1, 1, 1, 1, 1, 1, 34, 56, 56, 55, 137, 201, 201, 201, 201, 201, 201, 201, 56, 56, 33, 13, 13, 7, 7, 55, 137, 137, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 646 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580913 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580913 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580913/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580913 Building REAL300025580914 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580914' /scratch/stefan/7787361/working/building/REAL300025580914 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580914 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580914/0 /scratch/stefan/7787361/working/building/REAL300025580914 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/415 `/scratch/stefan/7787361/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2C(=O)N(C(C)C(=O)NCCC3=NC(=O)O[N-]3)C(=O)C2=C1) `REAL300025580914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580914 none CC1=CC=C2C(=O)N(C(C)C(=O)NCCC3=NC(=O)O[N-]3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 111, 59, 111, 59, 59, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 111, 111, 111, 59, 19, 19, 8, 8, 201] 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]) total number of confs: 609 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580914 none CC1=CC=C2C(=O)N(C(C)C(=O)NCCC3=NC(=O)O[N-]3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 33, 33, 33, 101, 112, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5, 33, 101, 101, 112, 112, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 21, 22, 23, 24, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580914 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580914 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580914/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580914 Building REAL300025580915 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580915' /scratch/stefan/7787361/working/building/REAL300025580915 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580915 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580915/0 /scratch/stefan/7787361/working/building/REAL300025580915 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/416 `/scratch/stefan/7787361/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580915 none CC(C)(C)OC(=O)N1CCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 188, 142, 188, 142, 142, 142, 73, 73, 73, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 142, 142, 142, 73, 22, 22, 8, 8] 201 rigid atoms, others: [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: 665 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580915 none CC(C)(C)OC(=O)N1CCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 10, 10, 10, 39, 56, 142, 142, 142, 142, 142, 10, 10, 10, 9, 9, 9, 10, 10, 10, 1, 1, 1, 1, 1, 10, 39, 39, 56, 56] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40]) total number of confs: 379 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580915 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580915 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580915/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580915 Building REAL300025580916 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580916' /scratch/stefan/7787361/working/building/REAL300025580916 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580916 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580916/0 /scratch/stefan/7787361/working/building/REAL300025580916 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/417 `/scratch/stefan/7787361/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Br) `REAL300025580916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580916 none CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 75, 75, 75, 24, 8, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 137, 75, 24, 24, 8, 8, 137] 137 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]) total number of confs: 342 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580916 none CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 12, 12, 12, 63, 88, 137, 137, 137, 137, 137, 1, 1, 1, 2, 2, 2, 12, 62, 62, 88, 88, 1] 137 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580916 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580916 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580916/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580916 Building REAL300025580917 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580917' /scratch/stefan/7787361/working/building/REAL300025580917 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580917 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580917/0 /scratch/stefan/7787361/working/building/REAL300025580917 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/418 `/scratch/stefan/7787361/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580917 none COC1=CC(Cl)=C(F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 175, 175, 175, 175, 175, 175, 175, 69, 69, 69, 20, 8, 1, 1, 1, 1, 1, 1, 1, 175, 201, 201, 201, 175, 68, 21, 20, 8, 8, 175] 201 rigid atoms, others: [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]) total number of confs: 420 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580917 none COC1=CC(Cl)=C(F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 58, 70, 175, 175, 175, 175, 175, 1, 3, 3, 3, 1, 12, 58, 58, 70, 70, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 24, 30] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580917 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580917 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580917/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580917 Building REAL300025580918 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580918' /scratch/stefan/7787361/working/building/REAL300025580918 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580918 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580918/0 /scratch/stefan/7787361/working/building/REAL300025580918 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/419 `/scratch/stefan/7787361/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC(F)=C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580918 none CC1=NN(C2=CC=CC(F)=C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 127, 127, 201, 201, 201, 201, 201, 201, 127, 70, 70, 70, 23, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 201, 201, 201, 201, 127, 70, 23, 23, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 456 number of broken/clashed sets: 32 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580918 none CC1=NN(C2=CC=CC(F)=C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 32, 33, 33, 107, 122, 201, 201, 201, 201, 201, 7, 7, 7, 1, 1, 1, 1, 7, 33, 107, 107, 122, 122] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 603 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580918 none CC1=NN(C2=CC=CC(F)=C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 1, 12, 12, 12, 50, 62, 127, 127, 127, 127, 127, 2, 2, 2, 7, 7, 6, 7, 1, 12, 50, 50, 62, 62] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 31] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 368 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580918 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580918 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580918/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580918 Building REAL300025580919 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580919' /scratch/stefan/7787361/working/building/REAL300025580919 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580919 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580919/0 /scratch/stefan/7787361/working/building/REAL300025580919 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/420 `/scratch/stefan/7787361/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCC1=NC(=O)O[N-]1)N1C(=O)C2=CC=CC=C2C1=O) `REAL300025580919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580919 none C[C@H](C(=O)NCCC1=NC(=O)O[N-]1)N1C(=O)C2=CC=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [4, 1, 4, 4, 22, 22, 22, 84, 102, 185, 185, 185, 185, 185, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 84, 84, 102, 102, 1, 1, 1, 1] 185 rigid atoms, others: [1, 34, 35, 36, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 554 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580919 none C[C@H](C(=O)NCCC1=NC(=O)O[N-]1)N1C(=O)C2=CC=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [192, 80, 192, 80, 80, 23, 8, 1, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 79, 24, 24, 8, 8, 192, 192, 192, 192] 192 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 743 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580919 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580919 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580919/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580919 Building REAL300025580920 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580920' /scratch/stefan/7787361/working/building/REAL300025580920 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580920 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580920/0 /scratch/stefan/7787361/working/building/REAL300025580920 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/421 `/scratch/stefan/7787361/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(OC(F)(F)F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580920 none CC(CC1=CC=C(OC(F)(F)F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 18, 56, 83, 83, 83, 83, 83, 201, 201, 201, 201, 83, 83, 18, 18, 8, 5, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 83, 83, 83, 83, 83, 83, 18, 8, 8, 5, 5] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 550 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580920 none CC(CC1=CC=C(OC(F)(F)F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 1, 1, 1, 1, 1, 1, 12, 17, 17, 17, 1, 1, 4, 12, 12, 12, 35, 37, 83, 83, 83, 83, 83, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 12, 35, 35, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 12, 13, 34, 31] set([0, 1, 8, 9, 10, 11, 14, 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: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580920 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580920 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580920/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580920 Building REAL300025580921 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580921' /scratch/stefan/7787361/working/building/REAL300025580921 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580921 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580921/0 /scratch/stefan/7787361/working/building/REAL300025580921 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/422 `/scratch/stefan/7787361/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)N=C2CCCN21) `REAL300025580921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580921 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)N=C2CCCN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 37, 62, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 62, 62, 1, 1, 1, 1, 1, 1] 159 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580921 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)N=C2CCCN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 20, 8, 1, 1, 1, 1, 1, 1, 1, 96, 159, 159, 159, 159, 159, 159, 159, 159, 96, 20, 20, 8, 8, 159, 159, 159, 159, 159, 159] 159 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580921 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580921 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580921/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580921 Building REAL300025580922 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580922' /scratch/stefan/7787361/working/building/REAL300025580922 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580922 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580922/0 /scratch/stefan/7787361/working/building/REAL300025580922 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/423 `/scratch/stefan/7787361/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)O2)C=N1) `REAL300025580922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580922 none CN1C=C(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)O2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 147, 147, 147, 147, 76, 76, 76, 22, 8, 1, 1, 1, 1, 1, 1, 1, 147, 201, 201, 201, 201, 201, 201, 147, 147, 76, 22, 22, 8, 8, 201] 201 rigid atoms, others: [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: 463 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580922 none CN1C=C(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)O2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 6, 6, 6, 35, 44, 147, 147, 147, 147, 147, 1, 12, 12, 13, 13, 13, 12, 1, 1, 6, 35, 35, 44, 44, 12] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 19, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 326 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580922 none CN1C=C(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)O2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 12, 36, 37, 37, 117, 135, 201, 201, 201, 201, 201, 12, 1, 1, 2, 2, 2, 1, 12, 12, 37, 117, 117, 135, 135, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 612 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580922 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580922 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580922/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580922 Building REAL300025580923 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580923' /scratch/stefan/7787361/working/building/REAL300025580923 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580923 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580923/0 /scratch/stefan/7787361/working/building/REAL300025580923 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/424 `/scratch/stefan/7787361/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=NN=C(C3=CC=CC=C3)N2C1) `REAL300025580923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580923 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=NN=C(C3=CC=CC=C3)N2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 5, 29, 29, 110, 123, 201, 201, 201, 201, 201, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 110, 110, 123, 123, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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, 41, 42]) total number of confs: 587 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580923 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=NN=C(C3=CC=CC=C3)N2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 55, 69, 197, 197, 197, 197, 197, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1, 10, 55, 55, 69, 69, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40]) total number of confs: 454 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580923 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=NN=C(C3=CC=CC=C3)N2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 61, 197, 197, 197, 197, 197, 197, 197, 201, 201, 197, 201, 201, 197, 197, 61, 19, 19, 8, 8, 197, 197, 197, 197, 197, 201, 201, 197, 201, 201, 197, 197] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 582 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580923 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580923 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580923/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580923 Building REAL300025580924 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580924' /scratch/stefan/7787361/working/building/REAL300025580924 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580924 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580924/0 /scratch/stefan/7787361/working/building/REAL300025580924 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/425 `/scratch/stefan/7787361/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC2=CC(Cl)=CC=C2N1)NCCC1=NC(=O)O[N-]1) `REAL300025580924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580924 none O=C(CC1=CC2=CC(Cl)=CC=C2N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 130, 201, 201, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 130, 130, 201, 201, 201, 201, 201, 51, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580924 none O=C(CC1=CC2=CC(Cl)=CC=C2N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 104, 106, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 35, 104, 104, 106, 106] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28] set([0, 1, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31]) total number of confs: 554 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580924 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580924 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580924/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580924 Building REAL300025580925 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580925' /scratch/stefan/7787361/working/building/REAL300025580925 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580925 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580925/0 /scratch/stefan/7787361/working/building/REAL300025580925 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/426 `/scratch/stefan/7787361/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C2=NN=C3CCC(C(=O)NCCC4=NC(=O)O[N-]4)CN32)=C1) `REAL300025580925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580925 none CC1=CC=CC(C2=NN=C3CCC(C(=O)NCCC4=NC(=O)O[N-]4)CN32)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 71, 71, 71, 71, 71, 71, 71, 30, 30, 30, 12, 7, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201, 201, 201, 201, 201, 201, 201, 71, 71, 71, 71, 71, 30, 12, 12, 7, 7, 71, 71, 201] 201 rigid atoms, others: [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]) total number of confs: 404 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580925 none CC1=CC=CC(C2=NN=C3CCC(C(=O)NCCC4=NC(=O)O[N-]4)CN32)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 37, 39, 71, 71, 71, 71, 71, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 9, 37, 37, 39, 39, 1, 1, 9] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 44, 43, 24, 25, 37] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 45]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580925 none CC1=CC=CC(C2=NN=C3CCC(C(=O)NCCC4=NC(=O)O[N-]4)CN32)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 41, 41, 41, 114, 117, 201, 201, 201, 201, 201, 9, 9, 1, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 41, 114, 114, 117, 117, 9, 9, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580925 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580925 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580925/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580925 Building REAL300025580926 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580926' /scratch/stefan/7787361/working/building/REAL300025580926 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580926 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580926/0 /scratch/stefan/7787361/working/building/REAL300025580926 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/427 `/scratch/stefan/7787361/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=C(Br)C=CC=C1OCC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580926 none N#CC1=C(Br)C=CC=C1OCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 17, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 181, 103, 33, 33, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 113, 113, 32, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 552 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580926 none N#CC1=C(Br)C=CC=C1OCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 17, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 56, 56, 56, 121, 121, 201, 201, 201, 201, 201, 1, 1, 1, 25, 25, 56, 121, 121, 121, 121] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 628 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580926 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580926 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580926/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580926 Building REAL300025580927 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580927' /scratch/stefan/7787361/working/building/REAL300025580927 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580927 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580927/0 /scratch/stefan/7787361/working/building/REAL300025580927 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/428 `/scratch/stefan/7787361/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C2=CC=CC=C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580927 none CN1N=C(C2=CC=CC=C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 181, 181, 181, 201, 201, 181, 201, 201, 181, 82, 82, 82, 24, 8, 1, 1, 1, 1, 1, 1, 1, 181, 181, 181, 201, 201, 181, 201, 201, 181, 82, 25, 25, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 510 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580927 none CN1N=C(C2=CC=CC=C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 7, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 41, 41, 41, 132, 152, 201, 201, 201, 201, 201, 7, 7, 7, 1, 1, 1, 1, 1, 7, 41, 132, 132, 152, 152] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36]) total number of confs: 689 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580927 none CN1N=C(C2=CC=CC=C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 1, 10, 10, 10, 53, 73, 181, 181, 181, 181, 181, 2, 2, 2, 7, 7, 1, 7, 7, 1, 10, 53, 53, 73, 73] 201 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 31] set([5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 462 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580927 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580927 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580927/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580927 Building REAL300025580928 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580928' /scratch/stefan/7787361/working/building/REAL300025580928 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580928 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580928/0 /scratch/stefan/7787361/working/building/REAL300025580928 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/429 `/scratch/stefan/7787361/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1) `REAL300025580928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580928 none CC(C)(C)OC(=O)NCCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 168, 201, 146, 112, 85, 25, 25, 25, 19, 19, 19, 7, 5, 1, 1, 1, 1, 1, 1, 1, 25, 25, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 146, 146, 112, 112, 85, 85, 25, 19, 7, 7, 5, 5] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 910 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580928 none CC(C)(C)OC(=O)NCCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 33, 23, 33, 17, 9, 5, 1, 1, 1, 1, 1, 3, 4, 4, 12, 13, 25, 25, 25, 25, 25, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 17, 17, 9, 9, 5, 5, 1, 4, 11, 11, 13, 13] 201 rigid atoms, others: [11, 10, 43, 12, 13, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580928 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580928 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580928/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580928 Building REAL300025580929 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580929' /scratch/stefan/7787361/working/building/REAL300025580929 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580929 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580929/0 /scratch/stefan/7787361/working/building/REAL300025580929 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/430 `/scratch/stefan/7787361/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(CC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580929 none CC(C)(C)OC(=O)NC(CC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 164, 164, 123, 164, 84, 27, 84, 122, 129, 129, 129, 129, 129, 27, 27, 12, 7, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 164, 164, 164, 164, 123, 84, 122, 122, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 27, 12, 12, 7, 7] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 861 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580929 none CC(C)(C)OC(=O)NC(CC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 10, 17, 6, 3, 1, 1, 1, 1, 1, 1, 1, 6, 21, 21, 21, 65, 66, 129, 129, 129, 129, 129, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 65, 65, 66, 66] 201 rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 15, 48, 49, 44, 46, 50, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 51, 52, 53, 54, 55]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580929 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580929 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580929/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580929 Building REAL300025580930 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580930' /scratch/stefan/7787361/working/building/REAL300025580930 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580930 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580930/0 /scratch/stefan/7787361/working/building/REAL300025580930 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/431 `/scratch/stefan/7787361/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)NC2=C(Cl)C=CC=C12) `REAL300025580930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580930 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)NC2=C(Cl)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 97, 97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 96, 25, 25, 8, 8, 192, 192, 192, 191] 192 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 439 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580930 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)NC2=C(Cl)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 68, 95, 192, 192, 192, 192, 192, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 67, 67, 95, 95, 1, 1, 1, 1] 192 rigid atoms, others: [0, 1, 2, 3, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 551 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580930 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580930 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580930/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580930 Building REAL300025580931 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580931' /scratch/stefan/7787361/working/building/REAL300025580931 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580931 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580931/0 /scratch/stefan/7787361/working/building/REAL300025580931 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/432 `/scratch/stefan/7787361/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(Br)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580931 none CN1N=CC(Br)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 197, 197, 197, 121, 121, 121, 24, 8, 1, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 121, 25, 25, 8, 8] 197 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]) total number of confs: 475 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580931 none CN1N=CC(Br)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 69, 197, 197, 197, 197, 197, 2, 2, 2, 1, 7, 39, 39, 69, 69] 197 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 485 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580931 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580931 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580931/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580931 Building REAL300025580932 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580932' /scratch/stefan/7787361/working/building/REAL300025580932 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580932 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580932/0 /scratch/stefan/7787361/working/building/REAL300025580932 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/433 `/scratch/stefan/7787361/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(CS(=O)(=O)CCC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580932 none CC1=CC=CC(CS(=O)(=O)CCC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 121, 201, 201, 121, 97, 80, 97, 97, 80, 41, 41, 41, 14, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 121, 201, 201, 121, 121, 80, 80, 80, 80, 41, 14, 14, 7, 7, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 927 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580932 none CC1=CC=CC(CS(=O)(=O)CCC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 13, 17, 17, 54, 54, 54, 117, 122, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 3, 3, 17, 17, 17, 17, 54, 117, 117, 122, 122, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 23, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 649 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580932 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580932 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580932/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580932 Building REAL300025580933 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580933' /scratch/stefan/7787361/working/building/REAL300025580933 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580933 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580933/0 /scratch/stefan/7787361/working/building/REAL300025580933 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/434 `/scratch/stefan/7787361/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)N[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C(C)C)C=C1) `REAL300025580933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580933 none CC1=CC=C(S(=O)(=O)N[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 191, 191, 191, 150, 191, 191, 120, 43, 120, 43, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 112, 139, 141, 191, 191, 191, 191, 191, 191, 191, 150, 42, 8, 8, 8, 8, 143, 143, 143, 143, 143, 143, 143, 191, 191] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 960 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580933 none CC1=CC=C(S(=O)(=O)N[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 26, 26, 26, 84, 86, 182, 182, 182, 182, 182, 10, 23, 23, 1, 1, 2, 2, 2, 1, 1, 6, 26, 84, 84, 86, 86, 23, 23, 23, 23, 23, 23, 23, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 46, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580933 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580933 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580933/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580933 Building REAL300025580934 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580934' /scratch/stefan/7787361/working/building/REAL300025580934 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580934 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580934/0 /scratch/stefan/7787361/working/building/REAL300025580934 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/435 `/scratch/stefan/7787361/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(Cl)C(Cl)=C1) `REAL300025580934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580934 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 33, 33, 110, 112, 201, 201, 201, 201, 201, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 33, 110, 110, 112, 112, 7, 7, 1, 1, 1] 201 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 542 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580934 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 59, 63, 143, 143, 143, 143, 143, 1, 1, 1, 1, 1, 1, 7, 7, 3, 7, 7, 7, 7, 13, 59, 59, 63, 63, 1, 1, 7, 7, 7] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 358 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580934 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 49, 143, 143, 143, 143, 143, 201, 201, 201, 201, 201, 201, 201, 49, 19, 19, 8, 8, 143, 143, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 538 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580934 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580934 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580934/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580934 Building REAL300025580935 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580935' /scratch/stefan/7787361/working/building/REAL300025580935 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580935 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580935/0 /scratch/stefan/7787361/working/building/REAL300025580935 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/436 `/scratch/stefan/7787361/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)N(CCC2=CC=C(F)C=C2)C1) `REAL300025580935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580935 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)N(CCC2=CC=C(F)C=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 44, 44, 107, 108, 201, 201, 201, 201, 201, 10, 10, 10, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 44, 107, 107, 108, 108, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43]) total number of confs: 549 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580935 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)N(CCC2=CC=C(F)C=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 47, 49, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 10, 1, 9, 47, 47, 49, 49, 1, 1, 1, 8, 8, 11, 11, 11, 11, 11, 11, 1, 1] 201 rigid atoms, others: [32, 1, 43, 33, 42, 11, 12, 13, 14, 15, 16, 25, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 356 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580935 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)N(CCC2=CC=C(F)C=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 50, 141, 141, 141, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 141, 50, 17, 17, 8, 8, 141, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 141, 141] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580935 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580935 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580935/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580935 Building REAL300025580936 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580936' /scratch/stefan/7787361/working/building/REAL300025580936 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580936 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580936/0 /scratch/stefan/7787361/working/building/REAL300025580936 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/437 `/scratch/stefan/7787361/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CSC2=CC=CC=C2O1)NCCC1=NC(=O)O[N-]1) `REAL300025580936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580936 none O=C(CC1CSC2=CC=CC=C2O1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 150, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 150, 150, 201, 201, 201, 201, 201, 201, 201, 51, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 757 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580936 none O=C(CC1CSC2=CC=CC=C2O1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 109, 111, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 36, 109, 109, 111, 111] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 34, 35, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580936 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580936 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580936/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580936 Building REAL300025580937 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580937' /scratch/stefan/7787361/working/building/REAL300025580937 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580937 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580937/0 /scratch/stefan/7787361/working/building/REAL300025580937 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/438 `/scratch/stefan/7787361/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)C2=CC=CC3=CC=CC=C32)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580937 none CN1C=C(C(=O)C2=CC=CC3=CC=CC=C32)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', '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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 66, 102, 102, 201, 201, 201, 201, 201, 201, 201, 201, 201, 66, 42, 42, 42, 17, 7, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 201, 201, 201, 201, 201, 201, 201, 66, 42, 17, 17, 7, 7] 201 rigid atoms, others: [22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 470 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580937 none CN1C=C(C(=O)C2=CC=CC3=CC=CC=C32)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', '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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 44, 44, 44, 129, 132, 201, 201, 201, 201, 201, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 20, 44, 129, 129, 132, 132] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 38, 39] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45]) total number of confs: 620 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580937 none CN1C=C(C(=O)C2=CC=CC3=CC=CC=C32)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', '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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 4, 4, 4, 20, 22, 66, 66, 66, 66, 66, 2, 2, 2, 1, 20, 20, 20, 20, 20, 20, 20, 1, 4, 20, 20, 22, 22] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 40, 16, 17, 18] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580937 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580937 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580937/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580937 Building REAL300025580938 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580938' /scratch/stefan/7787361/working/building/REAL300025580938 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580938 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580938/0 /scratch/stefan/7787361/working/building/REAL300025580938 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/439 `/scratch/stefan/7787361/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(CC2=CC=CC=C2)=C1) `REAL300025580938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580938 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(CC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 15, 40, 40, 106, 112, 201, 201, 201, 201, 201, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 14, 40, 106, 106, 112, 112, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 14] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39]) total number of confs: 585 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580938 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(CC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 33, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 1, 6, 14, 15, 7, 15, 14, 1, 5, 29, 29, 33, 33, 1, 1, 1, 6, 6, 15, 15, 7, 15, 15, 1] 201 rigid atoms, others: [1, 39, 11, 12, 13, 14, 15, 16, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580938 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(CC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 17, 8, 1, 1, 1, 1, 1, 1, 1, 39, 94, 94, 94, 94, 94, 201, 201, 201, 201, 201, 201, 94, 39, 17, 17, 8, 8, 94, 94, 94, 201, 201, 201, 201, 201, 201, 201, 94] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580938 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580938 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580938/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580938 Building REAL300025580939 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580939' /scratch/stefan/7787361/working/building/REAL300025580939 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580939 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580939/0 /scratch/stefan/7787361/working/building/REAL300025580939 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/440 `/scratch/stefan/7787361/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C[NH+]2CCCCC2)=C1) `REAL300025580939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580939 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C[NH+]2CCCCC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [23, 15, 23, 23, 67, 69, 122, 122, 122, 122, 122, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 23, 67, 67, 69, 69, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15] 122 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 45]) total number of confs: 354 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580939 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C[NH+]2CCCCC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 15, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 15, 15, 1, 3, 13, 13, 15, 15, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1] 122 rigid atoms, others: [32, 1, 45, 11, 12, 13, 14, 15, 16, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580939 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C[NH+]2CCCCC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 15, 7, 1, 1, 1, 1, 1, 1, 1, 33, 48, 48, 48, 48, 48, 87, 122, 122, 122, 122, 122, 122, 48, 33, 15, 15, 7, 7, 48, 48, 48, 87, 87, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 48] 122 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 490 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580939 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580939 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580939/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580939 Building REAL300025580940 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580940' /scratch/stefan/7787361/working/building/REAL300025580940 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580940 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580940/0 /scratch/stefan/7787361/working/building/REAL300025580940 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/441 `/scratch/stefan/7787361/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1[N+](=O)[O-]) `REAL300025580940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580940 none CC(C)OC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 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, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 141, 141, 141, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 141, 141, 201, 201, 201, 201, 201, 201, 201, 141, 49, 17, 17, 8, 8, 141, 141] 201 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, 37, 38]) total number of confs: 426 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580940 none CC(C)OC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 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, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 1, 1, 1, 1, 1, 5, 5, 5, 29, 33, 141, 141, 141, 141, 141, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 9, 1, 5, 29, 29, 33, 33, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 20, 21, 38, 37, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 284 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580940 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580940 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580940/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580940 Building REAL300025580941 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580941' /scratch/stefan/7787361/working/building/REAL300025580941 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580941 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580941/0 /scratch/stefan/7787361/working/building/REAL300025580941 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/442 `/scratch/stefan/7787361/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1) `REAL300025580941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580941 none CC1=CC=CC=C1N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 169, 169, 168, 90, 90, 90, 21, 8, 1, 1, 1, 1, 1, 1, 1, 169, 169, 201, 201, 201, 201, 201, 201, 201, 169, 89, 21, 21, 8, 8] 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]) total number of confs: 443 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580941 none CC1=CC=CC=C1N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 7, 8, 8, 1, 1, 1, 1, 1, 9, 9, 9, 36, 59, 169, 169, 169, 169, 169, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 9, 36, 36, 59, 59] 201 rigid atoms, others: [6, 7, 8, 9, 10, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580941 none CC1=CC=CC=C1N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 29, 29, 29, 92, 113, 201, 201, 201, 201, 201, 8, 8, 2, 2, 2, 1, 1, 1, 1, 8, 29, 92, 92, 113, 113] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 588 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580941 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580941 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580941/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580941 Building REAL300025580942 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580942' /scratch/stefan/7787361/working/building/REAL300025580942 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580942 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580942/0 /scratch/stefan/7787361/working/building/REAL300025580942 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/443 `/scratch/stefan/7787361/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(CC(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580942 none CCOC1=CC=C(CC(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 139, 139, 201, 201, 139, 106, 37, 106, 37, 37, 17, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 106, 106, 106, 106, 37, 17, 17, 7, 7, 201, 201] 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, 41, 42]) total number of confs: 1048 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580942 none CCOC1=CC=C(CC(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 2, 7, 7, 23, 23, 23, 71, 75, 201, 201, 201, 201, 201, 1, 1, 6, 6, 6, 6, 6, 1, 1, 2, 2, 7, 7, 7, 7, 23, 71, 71, 75, 75, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 41, 42, 21, 22, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 498 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580942 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580942 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580942/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580942 Building REAL300025580943 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580943' /scratch/stefan/7787361/working/building/REAL300025580943 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580943 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580943/0 /scratch/stefan/7787361/working/building/REAL300025580943 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/444 `/scratch/stefan/7787361/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C([N+](=O)[O-])C=C1) `REAL300025580943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580943 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 8, 11, 11, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 37, 37, 104, 116, 201, 201, 201, 201, 201, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 104, 104, 116, 116, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 570 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580943 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 8, 11, 11, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 67, 84, 181, 181, 181, 181, 181, 1, 1, 1, 1, 1, 1, 5, 5, 1, 3, 5, 5, 5, 5, 13, 67, 67, 84, 84, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 494 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580943 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 8, 11, 11, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 8, 1, 1, 1, 1, 1, 1, 1, 71, 181, 181, 181, 181, 181, 201, 201, 201, 201, 201, 201, 201, 201, 70, 23, 23, 8, 8, 181, 181, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 584 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580943 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580943 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580943/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580943 Building REAL300025580944 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580944' /scratch/stefan/7787361/working/building/REAL300025580944 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580944 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580944/0 /scratch/stefan/7787361/working/building/REAL300025580944 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/445 `/scratch/stefan/7787361/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(C(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C2O1) `REAL300025580944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580944 none CC1(C)CC(C(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 142, 77, 77, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 77, 25, 25, 8, 8, 142, 142, 142, 142] 142 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 459 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580944 none CC1(C)CC(C(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 42, 61, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 9, 42, 42, 61, 61, 1, 1, 1, 1] 142 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 37, 29, 30, 31] set([32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28]) total number of confs: 394 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580944 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580944 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580944/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580944 Building REAL300025580945 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580945' /scratch/stefan/7787361/working/building/REAL300025580945 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580945 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580945/0 /scratch/stefan/7787361/working/building/REAL300025580945 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/446 `/scratch/stefan/7787361/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580945 none CCC(CC)OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 201, 136, 201, 187, 28, 28, 74, 74, 28, 28, 28, 15, 7, 1, 1, 1, 1, 1, 1, 1, 74, 74, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 74, 74, 28, 15, 15, 7, 7, 74, 74] 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, 41, 42]) total number of confs: 929 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580945 none CCC(CC)OC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 4, 9, 10, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 74, 74, 74, 74, 74, 1, 1, 13, 13, 13, 13, 13, 9, 13, 13, 13, 13, 13, 1, 1, 5, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 21, 22, 41, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 246 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580945 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580945 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580945/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580945 Building REAL300025580946 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580946' /scratch/stefan/7787361/working/building/REAL300025580946 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580946 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580946/0 /scratch/stefan/7787361/working/building/REAL300025580946 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/447 `/scratch/stefan/7787361/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CC=C1OC1CCOC1)NCCC1=NC(=O)O[N-]1) `REAL300025580946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580946 none O=C(CC1=CC=CC=C1OC1CCOC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 101, 136, 136, 133, 136, 136, 136, 185, 201, 201, 201, 201, 11, 7, 1, 1, 1, 1, 1, 1, 1, 101, 101, 136, 136, 136, 136, 201, 201, 201, 201, 201, 201, 201, 29, 11, 11, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 598 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580946 none O=C(CC1=CC=CC=C1OC1CCOC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 13, 13, 13, 6, 13, 13, 6, 1, 1, 1, 1, 1, 1, 66, 66, 121, 121, 201, 201, 201, 201, 201, 28, 28, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 1, 66, 121, 121, 121, 121] 201 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 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, 29, 37, 38, 39, 40, 41]) total number of confs: 656 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580946 none O=C(CC1=CC=CC=C1OC1CCOC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 23, 23, 63, 63, 136, 136, 136, 136, 136, 5, 5, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 23, 63, 63, 63, 63] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580946 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580946 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580946/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580946 Building REAL300025580947 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580947' /scratch/stefan/7787361/working/building/REAL300025580947 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580947 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580947/0 /scratch/stefan/7787361/working/building/REAL300025580947 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/448 `/scratch/stefan/7787361/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CC=C1S(=O)(=O)C(F)F)NCCC1=NC(=O)O[N-]1) `REAL300025580947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580947 none O=C(CC1=CC=CC=C1S(=O)(=O)C(F)F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 3, 3, 3, 3, 3] 5 rigid atoms, others: [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]) total number of confs: 22 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580947 none O=C(CC1=CC=CC=C1S(=O)(=O)C(F)F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 3, 3, 3, 3, 3] 5 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 25 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580947 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580947 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580947/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580947 Building REAL300025580948 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580948' /scratch/stefan/7787361/working/building/REAL300025580948 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580948 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580948/0 /scratch/stefan/7787361/working/building/REAL300025580948 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/449 `/scratch/stefan/7787361/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2CCCCC2)=N1) `REAL300025580948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580948 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 5, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 12, 28, 28, 89, 108, 201, 201, 201, 201, 201, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 28, 89, 89, 108, 108, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 581 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580948 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 5, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 17, 29, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 3, 17, 17, 29, 29, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 21, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580948 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 5, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 24, 8, 1, 1, 1, 1, 1, 1, 1, 84, 111, 111, 111, 111, 201, 201, 201, 201, 201, 111, 84, 24, 24, 8, 8, 111, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 607 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580948 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580948 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580948/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580948 Building REAL300025580949 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580949' /scratch/stefan/7787361/working/building/REAL300025580949 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580949 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580949/0 /scratch/stefan/7787361/working/building/REAL300025580949 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/450 `/scratch/stefan/7787361/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(Cl)C=C1) `REAL300025580949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580949 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 31, 31, 108, 116, 201, 201, 201, 201, 201, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 31, 108, 108, 116, 116, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 566 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580949 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 56, 64, 136, 136, 136, 136, 136, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 13, 56, 56, 64, 64, 1, 1, 4, 4, 4, 4] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 356 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580949 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 9, 1, 1, 1, 1, 1, 1, 1, 54, 135, 136, 136, 136, 136, 201, 201, 136, 136, 201, 201, 54, 19, 19, 8, 8, 136, 136, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 686 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580949 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580949 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580949/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580949 Building REAL300025580950 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580950' /scratch/stefan/7787361/working/building/REAL300025580950 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580950 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580950/0 /scratch/stefan/7787361/working/building/REAL300025580950 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/451 `/scratch/stefan/7787361/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580950 none COC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 199, 201, 201, 153, 153, 153, 153, 47, 150, 47, 47, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 153, 153, 47, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 532 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580950 none COC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 57, 59, 153, 153, 153, 153, 153, 9, 9, 9, 6, 6, 6, 6, 1, 1, 13, 57, 57, 59, 59] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 372 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580950 none COC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 32, 32, 32, 107, 108, 201, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 1, 6, 6, 32, 107, 107, 108, 108] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 547 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580950 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580950 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580950/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580950 Building REAL300025580951 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580951' /scratch/stefan/7787361/working/building/REAL300025580951 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580951 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580951/0 /scratch/stefan/7787361/working/building/REAL300025580951 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/452 `/scratch/stefan/7787361/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1) `REAL300025580951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580951 none CCC1=CC=CC=C1N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 190, 190, 190, 190, 190, 127, 127, 127, 68, 68, 69, 20, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 201, 201, 201, 201, 201, 190, 190, 190, 190, 127, 68, 20, 20, 8, 8] 201 rigid atoms, others: [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: 507 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580951 none CCC1=CC=CC=C1N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 33, 42, 127, 127, 127, 127, 127, 1, 1, 9, 9, 9, 9, 9, 4, 3, 4, 4, 1, 7, 33, 33, 42, 42] 201 rigid atoms, others: [33, 7, 8, 9, 10, 11, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580951 none CCC1=CC=CC=C1N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 19, 19, 73, 86, 190, 190, 190, 190, 190, 3, 3, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 19, 73, 73, 86, 86] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 503 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580951 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580951 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580951/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580951 Building REAL300025580952 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580952' /scratch/stefan/7787361/working/building/REAL300025580952 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580952 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580952/0 /scratch/stefan/7787361/working/building/REAL300025580952 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/453 `/scratch/stefan/7787361/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=CN=C2)N=N1) `REAL300025580952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580952 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=CN=C2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 22, 22, 74, 95, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 74, 74, 95, 95, 7, 1, 1, 1, 1] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 535 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580952 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=CN=C2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 37, 50, 110, 111, 110, 111, 111, 1, 1, 1, 1, 7, 7, 6, 7, 7, 1, 1, 8, 36, 36, 50, 50, 1, 7, 7, 6, 7] 201 rigid atoms, others: [1, 11, 12, 13, 14, 20, 21, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 311 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580952 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=CN=C2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 21, 8, 1, 1, 1, 1, 1, 1, 1, 75, 111, 111, 111, 201, 201, 201, 201, 201, 110, 110, 74, 21, 21, 8, 8, 111, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 477 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580952 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580952 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580952/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580952 Building REAL300025580953 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580953' /scratch/stefan/7787361/working/building/REAL300025580953 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580953 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580953/0 /scratch/stefan/7787361/working/building/REAL300025580953 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/454 `/scratch/stefan/7787361/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC(C1=CC=C(O)C=C1)C1CC1)NCCC1=NC(=O)O[N-]1) `REAL300025580953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580953 none O=C(CC(C1=CC=C(O)C=C1)C1CC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 12, 1, 1, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 159, 159, 199, 201, 201, 402, 201, 201, 201, 201, 201, 201, 201, 46, 9, 8, 8, 8] 402 rigid atoms, others: [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]) total number of confs: 1216 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580953 none O=C(CC(C1=CC=C(O)C=C1)C1CC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 12, 1, 1, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [53, 16, 4, 1, 4, 8, 8, 4, 4, 8, 8, 1, 1, 1, 53, 53, 112, 112, 201, 201, 201, 201, 201, 16, 16, 4, 8, 8, 16, 8, 8, 1, 1, 1, 1, 1, 53, 112, 112, 112, 112] 402 rigid atoms, others: [32, 33, 34, 3, 11, 12, 13, 35, 31] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40]) total number of confs: 598 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580953 none O=C(CC(C1=CC=C(O)C=C1)C1CC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 12, 1, 1, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [57, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 57, 57, 120, 120, 201, 201, 201, 201, 201, 14, 14, 5, 1, 1, 2, 1, 1, 8, 8, 8, 8, 8, 57, 120, 120, 120, 120] 402 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580953 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580953 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580953/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580953 Building REAL300025580954 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580954' /scratch/stefan/7787361/working/building/REAL300025580954 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580954 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580954/0 /scratch/stefan/7787361/working/building/REAL300025580954 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/455 `/scratch/stefan/7787361/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C(Br)S1) `REAL300025580954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580954 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C(Br)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 8, 35, 35, 102, 115, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 35, 102, 102, 115, 115, 1, 1] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23]) total number of confs: 587 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580954 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C(Br)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 19, 8, 1, 1, 1, 1, 1, 1, 1, 67, 150, 150, 201, 201, 201, 201, 201, 67, 19, 19, 8, 8, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 570 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580954 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580954 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580954/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580954 Building REAL300025580955 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580955' /scratch/stefan/7787361/working/building/REAL300025580955 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580955 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580955/0 /scratch/stefan/7787361/working/building/REAL300025580955 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/456 `/scratch/stefan/7787361/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC(Cl)=CC=C1Cl) `REAL300025580955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580955 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC(Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 1, 1, 1, 16, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 6, 28, 28, 103, 105, 201, 201, 201, 201, 201, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 28, 103, 103, 105, 105, 1, 1, 1] 201 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26]) total number of confs: 566 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580955 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC(Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 1, 1, 1, 16, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 1, 1, 1, 1, 1, 1, 1, 47, 148, 148, 148, 192, 201, 201, 201, 201, 201, 201, 47, 15, 15, 7, 7, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 682 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580955 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580955 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580955/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580955 Building REAL300025580956 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580956' /scratch/stefan/7787361/working/building/REAL300025580956 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580956 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580956/0 /scratch/stefan/7787361/working/building/REAL300025580956 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/457 `/scratch/stefan/7787361/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1CC1=CC=CC=C1) `REAL300025580956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580956 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 13, 13, 13, 13, 32, 32, 32, 62, 62, 151, 151, 151, 151, 151, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 20, 20, 32, 62, 62, 62, 62, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580956 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 67, 67, 35, 35, 35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 66, 66, 67, 67, 140, 151, 151, 140, 151, 151, 110, 110, 110, 110, 110, 34, 8, 8, 8, 8, 140, 140, 151, 151, 151, 151, 151] 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, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 816 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580956 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 5, 5, 5, 19, 19, 66, 66, 66, 66, 66, 1, 1, 1, 1, 5, 13, 13, 6, 13, 13, 3, 3, 3, 2, 2, 5, 19, 19, 19, 19, 5, 5, 13, 13, 10, 13, 13] 201 rigid atoms, others: [1, 2, 3, 4, 15, 16, 17, 18] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580956 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580956 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580956/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580956 Building REAL300025580957 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580957' /scratch/stefan/7787361/working/building/REAL300025580957 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580957 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580957/0 /scratch/stefan/7787361/working/building/REAL300025580957 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/458 `/scratch/stefan/7787361/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580957 none COC(=O)C[C@H](NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 86, 126, 76, 57, 76, 76, 99, 143, 143, 155, 155, 155, 155, 57, 57, 20, 8, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 86, 86, 99, 155, 155, 155, 155, 155, 155, 155, 155, 155, 56, 20, 21, 8, 8] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 769 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580957 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580957 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580957/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580957 Building REAL300025580958 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580958' /scratch/stefan/7787361/working/building/REAL300025580958 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580958 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580958/0 /scratch/stefan/7787361/working/building/REAL300025580958 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/459 `/scratch/stefan/7787361/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2=C(F)C=CC=C2F)=N1) `REAL300025580958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580958 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2=C(F)C=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 28, 28, 86, 115, 201, 201, 201, 201, 201, 9, 9, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 28, 86, 86, 115, 115, 10, 1, 1, 1] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580958 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2=C(F)C=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 25, 36, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 7, 7, 7, 1, 7, 7, 7, 1, 6, 25, 25, 37, 37, 1, 7, 1, 7] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 23, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580958 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2=C(F)C=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 88, 134, 134, 134, 134, 201, 201, 201, 200, 201, 201, 201, 132, 88, 24, 24, 8, 8, 134, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 484 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580958 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580958 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580958/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580958 Building REAL300025580959 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580959' /scratch/stefan/7787361/working/building/REAL300025580959 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580959 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580959/0 /scratch/stefan/7787361/working/building/REAL300025580959 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/460 `/scratch/stefan/7787361/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)C2=CC=C(Cl)C=C2O1) `REAL300025580959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580959 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)C2=CC=C(Cl)C=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 1, 1, 1, 1, 16, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [12, 1, 12, 12, 59, 70, 158, 158, 158, 158, 158, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 59, 59, 70, 70, 1, 1, 1, 1] 158 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27]) total number of confs: 406 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580959 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)C2=CC=C(Cl)C=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 1, 1, 1, 1, 16, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [63, 63, 22, 8, 1, 1, 1, 1, 1, 1, 1, 63, 158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 63, 23, 23, 8, 8, 158, 158, 158, 158] 158 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 337 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580959 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580959 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580959/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580959 Building REAL300025580960 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580960' /scratch/stefan/7787361/working/building/REAL300025580960 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580960 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580960/0 /scratch/stefan/7787361/working/building/REAL300025580960 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/461 `/scratch/stefan/7787361/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1CCC1) `REAL300025580960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580960 none CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 27, 28, 28, 13, 7, 13, 3, 1, 3, 14, 14, 14, 48, 48, 121, 121, 121, 121, 121, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 3, 14, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [8, 41, 42, 43, 44, 45, 46, 40, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580960 none CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 178, 148, 178, 108, 38, 38, 38, 8, 8, 1, 1, 1, 1, 1, 1, 1, 104, 121, 121, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 108, 37, 8, 8, 8, 8, 121, 121, 121, 121, 121, 121, 121] 201 rigid atoms, others: [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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 763 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580960 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580960 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580960/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580960 Building REAL300025580961 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580961' /scratch/stefan/7787361/working/building/REAL300025580961 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580961 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580961/0 /scratch/stefan/7787361/working/building/REAL300025580961 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/462 `/scratch/stefan/7787361/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CCOC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025580961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580961 none CC(C)=CCOC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 192, 83, 83, 83, 83, 83, 67, 26, 26, 26, 11, 7, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 201, 194, 194, 83, 83, 83, 67, 67, 26, 11, 11, 7, 7, 83] 201 rigid atoms, others: [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: 493 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580961 none CC(C)=CCOC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 35, 37, 83, 83, 83, 83, 83, 1, 12, 12, 12, 12, 12, 12, 12, 10, 10, 1, 1, 1, 2, 2, 9, 35, 35, 37, 37, 1] 201 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 43, 23] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580961 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580961 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580961/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580961 Building REAL300025580962 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580962' /scratch/stefan/7787361/working/building/REAL300025580962 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580962 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580962/0 /scratch/stefan/7787361/working/building/REAL300025580962 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/463 `/scratch/stefan/7787361/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2F)C2=C1CCCC2) `REAL300025580962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580962 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2F)C2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 22, 22, 77, 103, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 77, 77, 103, 103, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 594 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580962 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2F)C2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 20, 34, 90, 90, 90, 90, 90, 1, 1, 1, 1, 8, 8, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 5, 20, 20, 34, 34, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580962 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2F)C2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 70, 90, 90, 90, 201, 201, 90, 201, 201, 201, 91, 91, 91, 91, 91, 91, 69, 24, 24, 8, 8, 201, 201, 201, 201, 91, 91, 91, 91, 91, 91, 91, 91] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 819 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580962 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580962 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580962/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580962 Building REAL300025580963 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580963' /scratch/stefan/7787361/working/building/REAL300025580963 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580963 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580963/0 /scratch/stefan/7787361/working/building/REAL300025580963 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/464 `/scratch/stefan/7787361/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(S(=O)(=O)C2CCC2)C=C1) `REAL300025580963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580963 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(S(=O)(=O)C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 25, 25, 109, 121, 201, 201, 201, 201, 201, 15, 15, 15, 8, 1, 8, 8, 1, 1, 1, 1, 15, 15, 25, 109, 109, 121, 121, 15, 15, 1, 1, 1, 1, 1, 1, 1, 15, 15] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39]) total number of confs: 599 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580963 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(S(=O)(=O)C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 21, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 2, 2, 2, 15, 15, 15, 1, 1, 3, 15, 15, 21, 21, 1, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1] 201 rigid atoms, others: [1, 38, 39, 11, 12, 13, 14, 15, 22, 23, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580963 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(S(=O)(=O)C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 63, 90, 90, 82, 90, 129, 129, 129, 201, 201, 201, 90, 90, 63, 19, 19, 8, 8, 90, 90, 201, 201, 201, 201, 201, 201, 201, 90, 90] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 802 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580963 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580963 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580963/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580963 Building REAL300025580964 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580964' /scratch/stefan/7787361/working/building/REAL300025580964 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580964 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580964/0 /scratch/stefan/7787361/working/building/REAL300025580964 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/465 `/scratch/stefan/7787361/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)(F)F)N=C2C=CC=CN21) `REAL300025580964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580964 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)(F)F)N=C2C=CC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 41, 63, 143, 143, 143, 143, 143, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 63, 63, 1, 1, 1, 1] 143 rigid atoms, others: [32, 1, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 24, 25, 26, 27, 28]) total number of confs: 395 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580964 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)(F)F)N=C2C=CC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 24, 8, 1, 1, 1, 1, 1, 1, 1, 71, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 71, 24, 24, 8, 8, 143, 143, 143, 143] 143 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580964 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580964 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580964/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580964 Building REAL300025580965 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580965' /scratch/stefan/7787361/working/building/REAL300025580965 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580965 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580965/0 /scratch/stefan/7787361/working/building/REAL300025580965 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/466 `/scratch/stefan/7787361/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1S(=O)(=O)C(F)F) `REAL300025580965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580965 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1S(=O)(=O)C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [3, 1, 3, 3, 7, 7, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 3, 7, 7, 7, 7, 1, 1, 1, 1, 5] 11 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580965 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1S(=O)(=O)C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 11, 11, 11, 11, 11] 11 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580965 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580965 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580965/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580965 Building REAL300025580966 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580966' /scratch/stefan/7787361/working/building/REAL300025580966 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580966 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580966/0 /scratch/stefan/7787361/working/building/REAL300025580966 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/467 `/scratch/stefan/7787361/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1COCC[C@@H]1C1=CC=CC=C1) `REAL300025580966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580966 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1COCC[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 12, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 3, 7, 7, 38, 59, 131, 131, 131, 131, 131, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 38, 38, 59, 59, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 131 rigid atoms, others: [36, 37, 38, 39, 40, 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]) total number of confs: 370 number of broken/clashed sets: 81 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580966 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1COCC[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 12, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 27, 46, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 5, 27, 27, 46, 46, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3] 131 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40]) total number of confs: 323 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580966 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1COCC[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 12, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [81, 81, 23, 9, 1, 1, 1, 1, 1, 1, 1, 81, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 80, 23, 23, 8, 8, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131] 131 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 410 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580966 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580966 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580966/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580966 Building REAL300025580967 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580967' /scratch/stefan/7787361/working/building/REAL300025580967 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580967 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580967/0 /scratch/stefan/7787361/working/building/REAL300025580967 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/468 `/scratch/stefan/7787361/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C=C1C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025580967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580967 none COC1=CC=C(Br)C=C1C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 176, 201, 201, 201, 176, 53, 53, 53, 19, 8, 1, 1, 1, 1, 1, 1, 1, 176, 176, 201, 201, 201, 201, 201, 201, 53, 19, 19, 8, 8, 176, 176, 176, 176] 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]) total number of confs: 673 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580967 none COC1=CC=C(Br)C=C1C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 11, 11, 11, 63, 71, 176, 176, 176, 176, 176, 1, 1, 8, 8, 8, 5, 3, 5, 11, 63, 63, 71, 71, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 439 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580967 none COC1=CC=C(Br)C=C1C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 23, 23, 23, 95, 100, 201, 201, 201, 201, 201, 5, 5, 4, 4, 4, 1, 1, 1, 23, 95, 95, 100, 100, 5, 5, 5, 5] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 528 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580967 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580967 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580967/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580967 Building REAL300025580968 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580968' /scratch/stefan/7787361/working/building/REAL300025580968 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580968 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580968/0 /scratch/stefan/7787361/working/building/REAL300025580968 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/469 `/scratch/stefan/7787361/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCCCN(CC(=O)NCCC2=NC(=O)O[N-]2)C1=O) `REAL300025580968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580968 none COC1CCCCN(CC(=O)NCCC2=NC(=O)O[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 181, 63, 63, 63, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 63, 22, 22, 8, 8] 201 rigid atoms, others: [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, 40]) total number of confs: 720 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580968 none COC1CCCCN(CC(=O)NCCC2=NC(=O)O[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 29, 99, 107, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 99, 99, 107, 107] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 20, 21, 25, 26, 27, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 581 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580968 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580968 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580968/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580968 Building REAL300025580969 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580969' /scratch/stefan/7787361/working/building/REAL300025580969 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580969 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580969/0 /scratch/stefan/7787361/working/building/REAL300025580969 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/470 `/scratch/stefan/7787361/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC=N1) `REAL300025580969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580969 none CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 19, 15, 19, 8, 1, 8, 24, 24, 24, 74, 76, 150, 150, 150, 150, 150, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 15, 8, 24, 74, 74, 76, 76, 1, 1] 201 rigid atoms, others: [8, 41, 42, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 451 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580969 none CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 192, 179, 135, 179, 111, 46, 46, 46, 19, 8, 1, 1, 1, 1, 1, 1, 1, 111, 150, 150, 150, 150, 192, 192, 192, 192, 192, 192, 192, 192, 192, 135, 111, 46, 19, 19, 8, 8, 150, 150] 201 rigid atoms, others: [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, 40, 41, 42]) total number of confs: 799 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580969 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580969 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580969/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580969 Building REAL300025580970 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580970' /scratch/stefan/7787361/working/building/REAL300025580970 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580970 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580970/0 /scratch/stefan/7787361/working/building/REAL300025580970 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/471 `/scratch/stefan/7787361/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C(=O)NCCC1=NC(=O)O[N-]1)C(C)NC(=O)OC(C)(C)C) `REAL300025580970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580970 none CC(C)C(C(=O)NCCC1=NC(=O)O[N-]1)C(C)NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 96, 108, 51, 51, 51, 19, 8, 1, 1, 1, 1, 1, 1, 1, 96, 98, 111, 138, 175, 175, 201, 201, 201, 201, 116, 116, 116, 116, 116, 116, 116, 96, 51, 19, 19, 8, 8, 111, 111, 111, 111, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 1012 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580970 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580970 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580970/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580970 Building REAL300025580971 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580971' /scratch/stefan/7787361/working/building/REAL300025580971 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580971 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580971/0 /scratch/stefan/7787361/working/building/REAL300025580971 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/472 `/scratch/stefan/7787361/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(C)(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025580971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580971 none CC(C)(C)OC(=O)N1CC(C)(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 139, 98, 139, 98, 98, 42, 98, 42, 42, 17, 8, 1, 1, 1, 1, 1, 1, 1, 98, 201, 201, 201, 201, 201, 201, 201, 201, 201, 98, 98, 98, 98, 98, 42, 17, 17, 8, 8, 98, 98] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 595 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580971 none CC(C)(C)OC(=O)N1CC(C)(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 34, 37, 98, 98, 98, 98, 98, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 7, 34, 34, 37, 37, 1, 1] 201 rigid atoms, others: [32, 33, 43, 5, 7, 8, 9, 10, 11, 22, 42] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 255 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580971 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580971 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580971/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580971 Building REAL300025580972 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580972' /scratch/stefan/7787361/working/building/REAL300025580972 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580972 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580972/0 /scratch/stefan/7787361/working/building/REAL300025580972 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/473 `/scratch/stefan/7787361/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(CC(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025580972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580972 none CC(C)(C)OC(=O)NCC1(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 186, 201, 161, 125, 80, 26, 26, 26, 10, 6, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 186, 161, 161, 80, 80, 26, 10, 10, 6, 6, 125, 125, 125, 125] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 803 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580972 none CC(C)(C)OC(=O)NCC1(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 13, 21, 5, 1, 1, 1, 6, 18, 18, 18, 60, 63, 125, 125, 125, 125, 125, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 13, 5, 5, 6, 6, 18, 60, 60, 63, 63, 1, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 43, 44, 45, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 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: 425 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580972 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580972 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580972/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580972 Building REAL300025580973 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580973' /scratch/stefan/7787361/working/building/REAL300025580973 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580973 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580973/0 /scratch/stefan/7787361/working/building/REAL300025580973 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/474 `/scratch/stefan/7787361/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(=O)OC(C)(C)C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025580973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580973 none CC(NC(=O)OC(C)(C)C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 70, 126, 176, 176, 201, 201, 201, 201, 56, 56, 56, 23, 23, 23, 12, 7, 1, 1, 1, 1, 1, 1, 1, 56, 56, 70, 70, 70, 70, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 56, 56, 23, 12, 12, 7, 7, 56, 56] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 644 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580973 none CC(NC(=O)OC(C)(C)C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 8, 14, 14, 17, 17, 17, 17, 1, 1, 1, 1, 1, 5, 5, 5, 19, 20, 56, 56, 56, 56, 56, 1, 1, 3, 3, 3, 3, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 5, 19, 19, 20, 20, 1, 1] 201 rigid atoms, others: [1, 41, 10, 11, 12, 13, 14, 48, 49, 25, 26, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580973 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580973 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580973/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580973 Building REAL300025580974 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580974' /scratch/stefan/7787361/working/building/REAL300025580974 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580974 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580974/0 /scratch/stefan/7787361/working/building/REAL300025580974 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/475 `/scratch/stefan/7787361/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2)C2=C1CCCC2) `REAL300025580974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580974 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2)C2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 23, 23, 81, 104, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 23, 81, 81, 104, 104, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 589 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580974 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2)C2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 32, 89, 89, 89, 88, 88, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 1, 1, 1, 1, 5, 19, 19, 32, 32, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580974 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2)C2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 66, 88, 88, 88, 201, 201, 201, 201, 201, 201, 88, 89, 89, 89, 89, 89, 66, 25, 25, 8, 8, 201, 201, 201, 201, 89, 89, 89, 89, 89, 89, 89, 88] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580974 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580974 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580974/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580974 Building REAL300025580975 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580975' /scratch/stefan/7787361/working/building/REAL300025580975 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580975 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580975/0 /scratch/stefan/7787361/working/building/REAL300025580975 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/476 `/scratch/stefan/7787361/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2F)C2=C1CCC2) `REAL300025580975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580975 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2F)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 22, 22, 80, 111, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 22, 80, 80, 111, 111, 1, 1, 1, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38, 39, 40]) total number of confs: 612 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580975 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2F)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 28, 43, 132, 132, 132, 132, 132, 1, 1, 1, 1, 8, 8, 7, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 28, 28, 43, 43, 8, 8, 8, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580975 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2F)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 24, 8, 1, 1, 1, 1, 1, 1, 1, 79, 132, 132, 132, 201, 201, 201, 201, 201, 201, 201, 132, 132, 132, 132, 132, 79, 24, 24, 8, 8, 201, 201, 201, 132, 132, 132, 132, 132, 132] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580975 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580975 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580975/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580975 Building REAL300025580976 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580976' /scratch/stefan/7787361/working/building/REAL300025580976 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580976 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580976/0 /scratch/stefan/7787361/working/building/REAL300025580976 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/477 `/scratch/stefan/7787361/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C(N2N=C(C(=O)NCCC3=NC(=O)O[N-]3)C3=C2CCC3)=C1) `REAL300025580976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580976 none CC1=CC=C(F)C(N2N=C(C(=O)NCCC3=NC(=O)O[N-]3)C3=C2CCC3)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 166, 201, 201, 201, 121, 121, 121, 73, 73, 73, 24, 8, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 201, 201, 201, 201, 201, 201, 73, 25, 25, 8, 8, 121, 121, 121, 121, 121, 121, 201] 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, 41, 42, 43]) total number of confs: 610 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580976 none CC1=CC=C(F)C(N2N=C(C(=O)NCCC3=NC(=O)O[N-]3)C3=C2CCC3)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 2, 8, 8, 8, 1, 1, 1, 1, 1, 9, 9, 9, 26, 39, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 8, 9, 26, 26, 39, 39, 1, 1, 1, 1, 1, 1, 8] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 39, 40, 41, 21, 22, 23, 24, 25, 38, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580976 none CC1=CC=C(F)C(N2N=C(C(=O)NCCC3=NC(=O)O[N-]3)C3=C2CCC3)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 80, 109, 201, 201, 201, 201, 201, 8, 8, 8, 8, 8, 1, 2, 2, 2, 1, 1, 23, 80, 80, 109, 109, 8, 8, 8, 8, 8, 8, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 26, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 613 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580976 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580976 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580976/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580976 Building REAL300025580977 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580977' /scratch/stefan/7787361/working/building/REAL300025580977 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580977 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580977/0 /scratch/stefan/7787361/working/building/REAL300025580977 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/478 `/scratch/stefan/7787361/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(F)=C1N1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C2=C1CCC2) `REAL300025580977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580977 none CC1=CC=CC(F)=C1N1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 194, 201, 201, 201, 143, 143, 143, 81, 81, 81, 23, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 201, 201, 201, 201, 201, 201, 81, 23, 23, 8, 8, 143, 143, 143, 143, 143, 143] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 499 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580977 none CC1=CC=CC(F)=C1N1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 2, 7, 7, 7, 1, 1, 1, 1, 1, 8, 8, 8, 30, 49, 143, 143, 143, 143, 143, 1, 1, 1, 1, 1, 7, 7, 7, 7, 5, 7, 8, 29, 29, 50, 50, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 38, 7, 8, 9, 10, 11, 40, 41, 22, 23, 24, 25, 26, 42, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 358 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580977 none CC1=CC=CC(F)=C1N1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 76, 111, 201, 201, 201, 201, 201, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 20, 76, 76, 111, 111, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 629 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580977 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580977 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580977/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580977 Building REAL300025580978 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580978' /scratch/stefan/7787361/working/building/REAL300025580978 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580978 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580978/0 /scratch/stefan/7787361/working/building/REAL300025580978 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/479 `/scratch/stefan/7787361/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2)C2=C1CCC2) `REAL300025580978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580978 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 24, 24, 80, 102, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 24, 80, 80, 102, 102, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40]) total number of confs: 569 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580978 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 24, 39, 121, 121, 121, 121, 121, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 1, 1, 1, 6, 23, 23, 39, 39, 7, 7, 6, 7, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580978 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(F)=C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 24, 8, 1, 1, 1, 1, 1, 1, 1, 70, 121, 121, 121, 201, 201, 201, 201, 201, 201, 121, 121, 121, 121, 121, 70, 24, 24, 8, 8, 201, 201, 201, 194, 121, 121, 121, 121, 121, 121] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580978 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580978 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580978/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580978 Building REAL300025580979 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580979' /scratch/stefan/7787361/working/building/REAL300025580979 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580979 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580979/0 /scratch/stefan/7787361/working/building/REAL300025580979 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/480 `/scratch/stefan/7787361/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025580979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580979 none CS(=O)(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 162, 201, 201, 162, 162, 162, 72, 72, 72, 21, 8, 1, 1, 1, 1, 1, 1, 1, 162, 201, 201, 201, 162, 162, 72, 21, 21, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 598 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580979 none CS(=O)(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 1, 1, 1, 1, 1, 11, 11, 11, 49, 63, 162, 162, 162, 162, 162, 1, 7, 7, 7, 1, 1, 11, 49, 49, 63, 63] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 19, 23, 24] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580979 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580979 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580979/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580979 Building REAL300025580980 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580980' /scratch/stefan/7787361/working/building/REAL300025580980 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580980 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580980/0 /scratch/stefan/7787361/working/building/REAL300025580980 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/481 `/scratch/stefan/7787361/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(CC(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C21) `REAL300025580980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580980 none CN1N=C(CC(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 39, 39, 39, 16, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 138, 39, 16, 16, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580980 none CN1N=C(CC(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 25, 25, 25, 96, 102, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 25, 96, 96, 102, 102, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 35, 32, 34, 16, 17, 18, 19, 20, 21] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 551 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580980 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580980 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580980/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580980 Building REAL300025580981 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580981' /scratch/stefan/7787361/working/building/REAL300025580981 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580981 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580981/0 /scratch/stefan/7787361/working/building/REAL300025580981 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/482 `/scratch/stefan/7787361/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C([N+](=O)[O-])C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580981 none CC1=CC(C)=C([N+](=O)[O-])C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 8, 11, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 77, 77, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 178, 178, 178, 178, 77, 25, 25, 8, 8] 178 rigid atoms, others: [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: 387 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580981 none CC1=CC(C)=C([N+](=O)[O-])C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 8, 11, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 10, 10, 10, 55, 85, 178, 178, 178, 178, 178, 2, 2, 2, 1, 2, 2, 2, 1, 10, 55, 55, 85, 85] 178 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 25, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580981 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580981 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580981/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580981 Building REAL300025580982 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580982' /scratch/stefan/7787361/working/building/REAL300025580982 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580982 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580982/0 /scratch/stefan/7787361/working/building/REAL300025580982 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/483 `/scratch/stefan/7787361/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)C2=CC(Br)=CC=C2O1) `REAL300025580982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580982 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)C2=CC(Br)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 1, 1, 1, 17, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [12, 1, 12, 12, 60, 74, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 60, 60, 74, 74, 1, 1, 1, 1] 133 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27]) total number of confs: 380 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580982 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)C2=CC(Br)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 1, 1, 1, 17, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [69, 69, 22, 8, 1, 1, 1, 1, 1, 1, 1, 69, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 69, 22, 22, 8, 8, 133, 133, 133, 133] 133 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 320 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580982 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580982 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580982/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580982 Building REAL300025580983 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580983' /scratch/stefan/7787361/working/building/REAL300025580983 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580983 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580983/0 /scratch/stefan/7787361/working/building/REAL300025580983 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/484 `/scratch/stefan/7787361/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1N1C=CC=N1) `REAL300025580983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580983 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1N1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 7, 8, 29, 29, 29, 98, 112, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 29, 98, 98, 112, 112, 8, 8, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 581 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580983 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1N1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 66, 66, 66, 20, 8, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 201, 201, 201, 201, 160, 160, 160, 160, 65, 20, 20, 8, 8, 160, 160, 201, 201, 201] 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, 34, 35, 36]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580983 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1N1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 29, 50, 160, 160, 160, 160, 160, 1, 1, 1, 1, 8, 8, 8, 8, 2, 2, 2, 1, 5, 29, 29, 50, 50, 1, 1, 8, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 15, 16, 17, 18, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580983 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580983 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580983/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580983 Building REAL300025580984 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580984' /scratch/stefan/7787361/working/building/REAL300025580984 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580984 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580984/0 /scratch/stefan/7787361/working/building/REAL300025580984 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/485 `/scratch/stefan/7787361/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC2=CC=NC=C2)C=C1) `REAL300025580984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580984 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC2=CC=NC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 34, 34, 96, 125, 201, 201, 201, 201, 201, 12, 19, 19, 12, 4, 1, 1, 1, 1, 1, 1, 1, 19, 19, 34, 96, 96, 125, 125, 19, 19, 4, 4, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [34, 35, 36, 37, 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, 38, 39]) total number of confs: 656 number of broken/clashed sets: 33 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580984 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC2=CC=NC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 27, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 2, 6, 19, 19, 19, 19, 19, 1, 1, 3, 15, 15, 27, 27, 1, 1, 6, 6, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [1, 38, 39, 11, 12, 13, 14, 15, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 238 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580984 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC2=CC=NC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 63, 20, 8, 1, 1, 1, 1, 1, 1, 1, 63, 89, 89, 63, 63, 113, 133, 201, 201, 201, 201, 201, 89, 89, 63, 20, 20, 8, 8, 89, 89, 133, 133, 201, 201, 201, 201, 89, 89] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 655 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580984 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580984 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580984/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580984 Building REAL300025580985 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580985' /scratch/stefan/7787361/working/building/REAL300025580985 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580985 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580985/0 /scratch/stefan/7787361/working/building/REAL300025580985 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/486 `/scratch/stefan/7787361/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NN(C2CCS(=O)(=O)C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580985 none CC(C)C1=NN(C2CCS(=O)(=O)C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 5, 5, 14, 11, 11, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 118, 118, 118, 201, 201, 201, 201, 201, 201, 118, 53, 53, 53, 19, 8, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 118, 118, 118, 201, 201, 201, 201, 201, 201, 201, 118, 53, 19, 19, 8, 8] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 535 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580985 none CC(C)C1=NN(C2CCS(=O)(=O)C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 5, 5, 14, 11, 11, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 38, 38, 38, 120, 126, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 38, 120, 120, 126, 126] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 39, 38, 37] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45]) total number of confs: 592 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580985 none CC(C)C1=NN(C2CCS(=O)(=O)C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 5, 5, 14, 11, 11, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 7, 7, 7, 38, 44, 118, 118, 118, 118, 118, 2, 2, 2, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 1, 7, 38, 38, 44, 44] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 13, 14, 15, 29] set([7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580985 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580985 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580985/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580985 Building REAL300025580986 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580986' /scratch/stefan/7787361/working/building/REAL300025580986 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580986 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580986/0 /scratch/stefan/7787361/working/building/REAL300025580986 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/487 `/scratch/stefan/7787361/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1CCOCC1) `REAL300025580986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580986 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 26, 26, 92, 110, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 26, 92, 92, 110, 110, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 581 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580986 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 45, 61, 164, 164, 164, 164, 164, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 8, 45, 45, 61, 61, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 409 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580986 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 8, 1, 1, 1, 1, 1, 1, 1, 75, 164, 164, 164, 164, 164, 201, 201, 201, 201, 201, 75, 20, 20, 8, 8, 164, 164, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 509 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580986 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580986 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580986/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580986 Building REAL300025580987 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580987' /scratch/stefan/7787361/working/building/REAL300025580987 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025580987 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580987/0 /scratch/stefan/7787361/working/building/REAL300025580987 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/488 `/scratch/stefan/7787361/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(F)(F)F)=C1[O-]) `REAL300025580987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580987 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(F)(F)F)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 1, 1, 1] 21 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580987 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(F)(F)F)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 21, 21, 21] 21 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580987 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025580987/1 /scratch/stefan/7787361/working/building/REAL300025580987 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/489 `/scratch/stefan/7787361/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(F)(F)F)=C1O) `REAL300025580987.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025580987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580987 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(F)(F)F)=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 302 conformations in input total number of sets (complete confs): 302 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 51, 68, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 51, 51, 68, 68, 1, 1, 1, 2] 302 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 30]) total number of confs: 407 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580987 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(F)(F)F)=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 302 conformations in input total number of sets (complete confs): 302 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 20, 8, 1, 1, 1, 1, 1, 1, 1, 76, 151, 151, 117, 151, 151, 151, 151, 151, 151, 151, 76, 20, 20, 8, 8, 151, 151, 151, 302] 302 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 790 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580987 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580987 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025580987/1.* 0: /scratch/stefan/7787361/working/building/REAL300025580987/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580987 Building REAL300025580988 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580988' /scratch/stefan/7787361/working/building/REAL300025580988 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580988 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580988/0 /scratch/stefan/7787361/working/building/REAL300025580988 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/490 `/scratch/stefan/7787361/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C2=NC(=O)O[N-]2)=C1) `REAL300025580988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580988 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 4, 18, 18, 67, 97, 201, 201, 201, 201, 201, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 18, 67, 67, 97, 97, 4, 4, 4, 4] 201 rigid atoms, others: [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]) total number of confs: 575 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580988 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 45, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 7, 29, 29, 45, 45, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580988 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 79, 126, 126, 126, 126, 126, 201, 201, 201, 201, 201, 126, 78, 23, 23, 8, 8, 126, 126, 126, 126] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580988 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580988 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580988/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580988 Building REAL300025580989 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580989' /scratch/stefan/7787361/working/building/REAL300025580989 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580989 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580989/0 /scratch/stefan/7787361/working/building/REAL300025580989 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/491 `/scratch/stefan/7787361/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=C(F)C=CC=C2F)CCC1) `REAL300025580989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580989 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=C(F)C=CC=C2F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 3, 16, 16, 72, 106, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 72, 72, 106, 106, 1, 1, 1, 3, 3, 3, 3, 3, 3] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 612 number of broken/clashed sets: 36 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580989 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=C(F)C=CC=C2F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 67, 103, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 2, 4, 4, 4, 1, 1, 1, 12, 67, 67, 103, 103, 4, 2, 4, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 33, 11, 12, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 609 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580989 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=C(F)C=CC=C2F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 23, 23, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 602 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580989 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580989 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580989/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580989 Building REAL300025580990 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580990' /scratch/stefan/7787361/working/building/REAL300025580990 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580990 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580990/0 /scratch/stefan/7787361/working/building/REAL300025580990 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/492 `/scratch/stefan/7787361/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL300025580990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580990 none CCOC(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 14, 12, 4, 12, 1, 4, 9, 9, 9, 28, 35, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 4, 9, 28, 28, 35, 35, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 17, 18, 19, 20, 21, 22, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580990 none CCOC(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 188, 187, 114, 187, 62, 62, 62, 22, 8, 1, 1, 1, 1, 1, 1, 1, 114, 115, 115, 114, 115, 115, 201, 201, 201, 201, 201, 114, 62, 22, 22, 8, 8, 115, 115, 115, 115, 115] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 776 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580990 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580990 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580990/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580990 Building REAL300025580991 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580991' /scratch/stefan/7787361/working/building/REAL300025580991 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580991 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580991/0 /scratch/stefan/7787361/working/building/REAL300025580991 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/493 `/scratch/stefan/7787361/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1) `REAL300025580991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580991 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 4, 23, 23, 73, 76, 173, 173, 173, 173, 173, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 4, 4, 23, 73, 73, 76, 76, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 447 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580991 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 52, 60, 154, 154, 154, 154, 154, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 6, 6, 6, 6, 1, 1, 12, 51, 51, 60, 60, 4, 4, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1] 201 rigid atoms, others: [1, 11, 12, 13, 46, 19, 20, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 388 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580991 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 1, 1, 1, 1, 1, 1, 1, 63, 154, 154, 173, 173, 160, 173, 173, 154, 154, 201, 201, 201, 201, 154, 154, 62, 21, 21, 8, 8, 173, 173, 160, 173, 173, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 602 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580991 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 35, 35, 89, 94, 201, 201, 201, 201, 201, 6, 6, 6, 14, 14, 10, 14, 14, 1, 1, 1, 1, 1, 1, 6, 6, 35, 89, 89, 94, 94, 14, 14, 10, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 546 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580991 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580991 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580991/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580991 Building REAL300025580992 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580992' /scratch/stefan/7787361/working/building/REAL300025580992 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580992 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580992/0 /scratch/stefan/7787361/working/building/REAL300025580992 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/494 `/scratch/stefan/7787361/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(S(=O)(=O)C(F)F)=C1) `REAL300025580992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580992 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(S(=O)(=O)C(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 39, 132, 132, 132, 132, 132, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 18, 1, 5, 29, 29, 39, 39, 1, 1, 1, 17, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 22, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31]) total number of confs: 343 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580992 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(S(=O)(=O)C(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 56, 132, 132, 132, 132, 132, 161, 161, 161, 201, 201, 132, 56, 17, 17, 8, 8, 132, 132, 132, 201, 132] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580992 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580992 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580992/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580992 Building REAL300025580993 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580993' /scratch/stefan/7787361/working/building/REAL300025580993 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580993 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580993/0 /scratch/stefan/7787361/working/building/REAL300025580993 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/495 `/scratch/stefan/7787361/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NSC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1) `REAL300025580993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580993 none O=C(CC1=NSC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 14, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 154, 201, 201, 201, 201, 201, 201, 201, 201, 21, 8, 1, 1, 1, 1, 1, 1, 1, 154, 154, 201, 201, 201, 201, 59, 21, 21, 8, 8] 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]) total number of confs: 680 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580993 none O=C(CC1=NSC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 14, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 101, 107, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 30, 101, 101, 107, 107] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 566 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580993 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580993 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580993/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580993 Building REAL300025580994 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580994' /scratch/stefan/7787361/working/building/REAL300025580994 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580994 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580994/0 /scratch/stefan/7787361/working/building/REAL300025580994 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/496 `/scratch/stefan/7787361/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC3=CC=CC=C3C=C2)=NN1) `REAL300025580994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580994 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC3=CC=CC=C3C=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 13, 42, 42, 129, 147, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 42, 129, 129, 147, 147, 13, 1, 1, 1, 1, 1, 1, 1, 13] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 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, 39]) total number of confs: 646 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580994 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC3=CC=CC=C3C=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 28, 38, 97, 97, 97, 97, 97, 1, 1, 1, 1, 13, 13, 13, 13, 13, 12, 12, 13, 13, 1, 1, 6, 28, 28, 38, 38, 1, 13, 13, 13, 13, 13, 13, 13, 1] 201 rigid atoms, others: [1, 39, 11, 12, 13, 14, 24, 25, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580994 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC3=CC=CC=C3C=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 19, 8, 1, 1, 1, 1, 1, 1, 1, 56, 97, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 56, 19, 19, 8, 8, 97, 201, 201, 201, 201, 201, 201, 201, 97] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580994 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580994 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580994/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580994 Building REAL300025580995 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580995' /scratch/stefan/7787361/working/building/REAL300025580995 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580995 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580995/0 /scratch/stefan/7787361/working/building/REAL300025580995 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/497 `/scratch/stefan/7787361/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025580995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580995 none CC1=C(Br)C=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [177, 178, 178, 178, 178, 80, 80, 80, 24, 8, 1, 1, 1, 1, 1, 1, 1, 177, 178, 178, 178, 178, 79, 24, 24, 8, 8] 178 rigid atoms, others: [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]) total number of confs: 402 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580995 none CC1=C(Br)C=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 65, 102, 177, 177, 177, 177, 177, 1, 2, 2, 2, 1, 12, 65, 65, 102, 102] 178 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 21] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580995 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580995 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580995/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580995 Building REAL300025580996 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580996' /scratch/stefan/7787361/working/building/REAL300025580996 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580996 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580996/0 /scratch/stefan/7787361/working/building/REAL300025580996 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/498 `/scratch/stefan/7787361/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(Cl)=C2F)C2=C1CCC2) `REAL300025580996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580996 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(Cl)=C2F)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 15, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 23, 23, 77, 104, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 23, 77, 77, 104, 104, 1, 1, 1, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38, 39, 40]) total number of confs: 597 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580996 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(Cl)=C2F)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 15, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 27, 44, 130, 130, 130, 130, 130, 1, 1, 1, 1, 8, 8, 7, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 27, 27, 44, 44, 8, 8, 8, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580996 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC(Cl)=C2F)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 15, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 77, 130, 130, 130, 201, 201, 201, 201, 201, 201, 201, 130, 130, 130, 130, 130, 77, 25, 25, 8, 8, 201, 201, 201, 130, 130, 130, 130, 130, 130] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580996 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580996 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580996/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580996 Building REAL300025580997 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580997' /scratch/stefan/7787361/working/building/REAL300025580997 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580997 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580997/0 /scratch/stefan/7787361/working/building/REAL300025580997 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/499 `/scratch/stefan/7787361/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC1=CC=CC=C1C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025580997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580997 none CCC(CC1=CC=CC=C1C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 106, 48, 108, 163, 201, 201, 198, 201, 201, 201, 49, 49, 8, 8, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 127, 108, 163, 163, 201, 201, 163, 201, 201, 201, 201, 48, 8, 8, 8, 8] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 987 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580997 none CCC(CC1=CC=CC=C1C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 36, 36, 36, 106, 106, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 10, 5, 5, 1, 1, 1, 1, 2, 2, 2, 36, 106, 106, 106, 106] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 604 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580997 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580997 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580997/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580997 Building REAL300025580998 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580998' /scratch/stefan/7787361/working/building/REAL300025580998 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580998 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580998/0 /scratch/stefan/7787361/working/building/REAL300025580998 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/500 `/scratch/stefan/7787361/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC(N2N=C(C(=O)NCCC3=NC(=O)O[N-]3)C3=C2CCC3)=C1) `REAL300025580998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580998 none CC1=CC(F)=CC(N2N=C(C(=O)NCCC3=NC(=O)O[N-]3)C3=C2CCC3)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 112, 112, 112, 72, 72, 72, 23, 8, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 201, 201, 201, 201, 201, 201, 72, 23, 23, 8, 8, 112, 112, 112, 112, 112, 112, 201] 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, 41, 42, 43]) total number of confs: 465 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580998 none CC1=CC(F)=CC(N2N=C(C(=O)NCCC3=NC(=O)O[N-]3)C3=C2CCC3)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 6, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 6, 23, 36, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 22, 22, 36, 36, 1, 1, 1, 1, 1, 1, 7] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 39, 40, 41, 21, 22, 23, 24, 25, 38, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580998 none CC1=CC(F)=CC(N2N=C(C(=O)NCCC3=NC(=O)O[N-]3)C3=C2CCC3)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 24, 24, 80, 113, 201, 201, 201, 201, 201, 7, 7, 7, 7, 7, 1, 2, 2, 2, 1, 1, 24, 80, 80, 113, 113, 7, 7, 7, 7, 7, 7, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 26, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 642 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580998 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580998 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580998/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580998 Building REAL300025580999 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025580999' /scratch/stefan/7787361/working/building/REAL300025580999 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025580999 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025580999/0 /scratch/stefan/7787361/working/building/REAL300025580999 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/501 `/scratch/stefan/7787361/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(N2C=NN=C2)C=C1)NCCC1=NC(=O)O[N-]1) `REAL300025580999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025580999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025580999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580999 none O=C(CC1=CC=C(N2C=NN=C2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 135, 135, 201, 201, 201, 201, 201, 201, 49, 17, 17, 8, 8] 201 rigid atoms, others: [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: 660 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580999 none O=C(CC1=CC=C(N2C=NN=C2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 4, 2, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 17, 17, 82, 97, 201, 201, 201, 201, 201, 8, 8, 4, 4, 1, 1, 4, 4, 17, 82, 82, 97, 97] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 569 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025580999 none O=C(CC1=CC=C(N2C=NN=C2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 9, 9, 57, 77, 201, 201, 201, 201, 201, 4, 4, 1, 1, 3, 3, 1, 1, 9, 57, 57, 77, 77] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 12, 13, 25, 26, 29, 30] set([0, 1, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 516 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025580999 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025580999 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025580999/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025580999 Building REAL300025581000 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581000' /scratch/stefan/7787361/working/building/REAL300025581000 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581000 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581000/0 /scratch/stefan/7787361/working/building/REAL300025581000 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/502 `/scratch/stefan/7787361/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=CC(OC(F)F)=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581000 none O=C(CCC1=CC=CC(OC(F)F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 45, 45, 81, 81, 81, 81, 81, 191, 201, 201, 81, 7, 5, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 81, 81, 81, 201, 81, 9, 7, 7, 5, 5] 201 rigid atoms, others: [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]) total number of confs: 466 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581000 none O=C(CCC1=CC=CC(OC(F)F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 11, 11, 1, 19, 19, 39, 39, 81, 81, 81, 81, 81, 2, 2, 2, 2, 1, 1, 1, 11, 1, 19, 39, 39, 39, 39] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 13, 27, 28, 29, 31] set([0, 1, 2, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 32, 33, 34, 35, 36]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581000 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581000 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581000/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581000 Building REAL300025581001 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581001' /scratch/stefan/7787361/working/building/REAL300025581001 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581001 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581001/0 /scratch/stefan/7787361/working/building/REAL300025581001 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/503 `/scratch/stefan/7787361/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(Br)O1) `REAL300025581001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581001 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(Br)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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: [186, 186, 94, 94, 94, 20, 8, 1, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 186, 186, 94, 21, 21, 8, 8, 186] 186 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 426 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581001 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(Br)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 11, 11, 11, 61, 97, 186, 186, 186, 186, 186, 1, 1, 1, 1, 2, 2, 2, 11, 61, 61, 97, 97, 1] 186 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 556 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581001 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581001 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581001/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581001 Building REAL300025581002 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581002' /scratch/stefan/7787361/working/building/REAL300025581002 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581002 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581002/0 /scratch/stefan/7787361/working/building/REAL300025581002 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/504 `/scratch/stefan/7787361/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025581002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581002 none CC(=O)NC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 167, 167, 167, 167, 167, 138, 63, 63, 63, 19, 8, 1, 1, 1, 1, 1, 1, 1, 167, 201, 201, 201, 201, 167, 167, 167, 138, 138, 63, 19, 19, 8, 8, 167] 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]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581002 none CC(=O)NC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 44, 62, 167, 167, 167, 167, 167, 1, 4, 4, 4, 4, 1, 1, 1, 4, 4, 11, 44, 44, 62, 62, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 21, 36, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 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 /scratch/stefan/7787361/working/building/REAL300025581002 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581002 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581002/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581002 Building REAL300025581003 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581003' /scratch/stefan/7787361/working/building/REAL300025581003 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581003 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581003/0 /scratch/stefan/7787361/working/building/REAL300025581003 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/505 `/scratch/stefan/7787361/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CC2CCC1C(C(=O)NCCC1=NC(=O)O[N-]1)C2) `REAL300025581003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581003 none COC(=O)N1CC2CCC1C(C(=O)NCCC1=NC(=O)O[N-]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 144, 201, 144, 144, 144, 144, 144, 144, 68, 68, 68, 22, 8, 1, 1, 1, 1, 1, 1, 1, 144, 201, 201, 201, 144, 144, 144, 144, 144, 144, 144, 144, 144, 68, 23, 22, 8, 8, 144, 144] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 684 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581003 none COC(=O)N1CC2CCC1C(C(=O)NCCC1=NC(=O)O[N-]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 40, 51, 144, 144, 144, 144, 144, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 40, 40, 51, 51, 1, 1] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 34, 40, 22, 41, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 36, 37, 35, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 38]) total number of confs: 338 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581003 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581003 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581003/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581003 Building REAL300025581004 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581004' /scratch/stefan/7787361/working/building/REAL300025581004 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581004 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581004/0 /scratch/stefan/7787361/working/building/REAL300025581004 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/506 `/scratch/stefan/7787361/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CC2C=CC1C(C(=O)NCCC1=NC(=O)O[N-]1)C2) `REAL300025581004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581004 none COC(=O)N1CC2C=CC1C(C(=O)NCCC1=NC(=O)O[N-]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 142, 201, 142, 142, 142, 142, 142, 142, 66, 66, 66, 23, 8, 1, 1, 1, 1, 1, 1, 1, 142, 201, 201, 201, 142, 142, 142, 142, 142, 142, 142, 66, 23, 23, 8, 8, 142, 142] 201 rigid atoms, others: [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]) total number of confs: 680 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581004 none COC(=O)N1CC2C=CC1C(C(=O)NCCC1=NC(=O)O[N-]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 46, 61, 142, 142, 142, 142, 142, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 46, 46, 61, 61, 1, 1] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 11, 38, 22, 39, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 3, 36, 37, 35, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25]) total number of confs: 376 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581004 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581004 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581004/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581004 Building REAL300025581005 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581005' /scratch/stefan/7787361/working/building/REAL300025581005 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581005 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581005/0 /scratch/stefan/7787361/working/building/REAL300025581005 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/507 `/scratch/stefan/7787361/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@H]1C2CCC(CC2)[C@@H]1C(F)(F)F) `REAL300025581005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581005 none O=C(NCCC1=NC(=O)O[N-]1)[C@H]1C2CCC(CC2)[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 39, 54, 124, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 39, 39, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 124 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 338 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581005 none O=C(NCCC1=NC(=O)O[N-]1)[C@H]1C2CCC(CC2)[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 23, 9, 1, 1, 1, 1, 1, 1, 1, 71, 124, 124, 124, 124, 124, 124, 124, 124, 124, 124, 124, 124, 124, 71, 23, 23, 9, 9, 124, 124, 124, 124, 124, 124, 124, 124, 124, 124] 124 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 408 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581005 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581005 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581005/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581005 Building REAL300025581006 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581006' /scratch/stefan/7787361/working/building/REAL300025581006 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581006 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581006/0 /scratch/stefan/7787361/working/building/REAL300025581006 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/508 `/scratch/stefan/7787361/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=C(Cl)C=C2Cl)CCCCC1) `REAL300025581006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581006 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=C(Cl)C=C2Cl)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 3, 7, 7, 31, 57, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 31, 31, 57, 57, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 137 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 381 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581006 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=C(Cl)C=C2Cl)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 4, 28, 54, 134, 134, 135, 134, 134, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 4, 28, 28, 54, 54, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 137 rigid atoms, others: [1, 34, 35, 36, 37, 38, 33, 40, 41, 42, 11, 12, 20, 21, 22, 23, 24, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 372 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581006 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=C(Cl)C=C2Cl)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [56, 56, 22, 8, 1, 1, 1, 1, 1, 1, 1, 56, 134, 137, 137, 137, 137, 137, 137, 137, 134, 135, 135, 135, 135, 55, 23, 22, 8, 8, 137, 137, 137, 134, 134, 135, 135, 135, 135, 135, 135, 135, 135] 137 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 430 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581006 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581006 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581006/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581006 Building REAL300025581007 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581007' /scratch/stefan/7787361/working/building/REAL300025581007 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581007 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581007/0 /scratch/stefan/7787361/working/building/REAL300025581007 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/509 `/scratch/stefan/7787361/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(CCCC#N)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581007 none CC(C)(C)OC(=O)NC(CCCC#N)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 126, 115, 126, 86, 34, 86, 150, 150, 181, 181, 34, 34, 13, 7, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126, 126, 126, 126, 115, 86, 150, 150, 150, 150, 181, 181, 34, 13, 13, 7, 7] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1001 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581007 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581007 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581007/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581007 Building REAL300025581008 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581008' /scratch/stefan/7787361/working/building/REAL300025581008 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581008 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581008/0 /scratch/stefan/7787361/working/building/REAL300025581008 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/510 `/scratch/stefan/7787361/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1C[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581008 none CC(C)(C)OC(=O)N[C@@H]1C[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 165, 116, 165, 98, 98, 98, 98, 39, 98, 39, 39, 16, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 98, 98, 39, 16, 16, 8, 8] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 626 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581008 none CC(C)(C)OC(=O)N[C@@H]1C[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 39, 98, 98, 98, 98, 98, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 1, 1, 9, 37, 37, 39, 39] 201 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581008 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581008 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581008/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581008 Building REAL300025581009 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581009' /scratch/stefan/7787361/working/building/REAL300025581009 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581009 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581009/0 /scratch/stefan/7787361/working/building/REAL300025581009 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/511 `/scratch/stefan/7787361/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NN(C2=CC=CC=C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581009 none CC(C)C1=NN(C2=CC=CC=C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 76, 76, 76, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 22, 22, 8, 8] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 413 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581009 none CC(C)C1=NN(C2=CC=CC=C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 21, 22, 22, 74, 98, 201, 201, 201, 201, 201, 4, 4, 4, 3, 4, 4, 4, 1, 1, 1, 1, 1, 4, 22, 74, 74, 98, 98] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42]) total number of confs: 566 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581009 none CC(C)C1=NN(C2=CC=CC=C2)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 9, 9, 10, 50, 76, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 10, 50, 50, 76, 76] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 37, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 518 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581009 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581009 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581009/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581009 Building REAL300025581010 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581010' /scratch/stefan/7787361/working/building/REAL300025581010 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581010 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581010/0 /scratch/stefan/7787361/working/building/REAL300025581010 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/512 `/scratch/stefan/7787361/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2(C(=O)NCCC3=NC(=O)O[N-]3)CCC2)C=C1) `REAL300025581010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581010 none CC1=CC=C(C2(C(=O)NCCC3=NC(=O)O[N-]3)CCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 201, 201, 181, 76, 76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 181, 181, 181, 201, 201, 201, 201, 201, 201, 201, 75, 24, 24, 8, 8, 181, 181, 181, 181, 181, 181, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 770 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581010 none CC1=CC=C(C2(C(=O)NCCC3=NC(=O)O[N-]3)CCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 12, 12, 12, 62, 86, 181, 181, 181, 181, 181, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 62, 62, 86, 86, 1, 1, 1, 1, 1, 1, 4, 4] 201 rigid atoms, others: [34, 35, 4, 5, 6, 32, 17, 18, 19, 36, 33, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39]) total number of confs: 514 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581010 none CC1=CC=C(C2(C(=O)NCCC3=NC(=O)O[N-]3)CCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 24, 24, 24, 87, 112, 201, 201, 201, 201, 201, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1, 24, 87, 87, 112, 112, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 600 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581010 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581010 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581010/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581010 Building REAL300025581011 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581011' /scratch/stefan/7787361/working/building/REAL300025581011 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581011 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581011/0 /scratch/stefan/7787361/working/building/REAL300025581011 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/513 `/scratch/stefan/7787361/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC=CC(Cl)=C1Cl) `REAL300025581011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581011 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 1, 1, 1, 1, 1, 16, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 32, 32, 95, 100, 201, 201, 201, 201, 201, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 32, 95, 95, 100, 100, 1, 1, 1] 201 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26]) total number of confs: 551 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581011 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 1, 1, 1, 1, 1, 16, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 1, 1, 1, 1, 1, 1, 1, 46, 150, 150, 150, 195, 201, 201, 201, 201, 201, 201, 46, 17, 17, 7, 7, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 692 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581011 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581011 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581011/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581011 Building REAL300025581012 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581012' /scratch/stefan/7787361/working/building/REAL300025581012 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581012 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581012/0 /scratch/stefan/7787361/working/building/REAL300025581012 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/514 `/scratch/stefan/7787361/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(SC(F)(F)F)O1) `REAL300025581012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581012 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(SC(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 5, 15, 15, 15, 12, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 34, 43, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 11, 25, 25, 25, 1, 6, 34, 34, 44, 44, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 20, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 335 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581012 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(SC(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 5, 15, 15, 15, 12, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 59, 111, 111, 111, 111, 201, 201, 201, 201, 111, 59, 23, 23, 8, 8, 111, 111] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581012 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581012 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581012/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581012 Building REAL300025581013 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581013' /scratch/stefan/7787361/working/building/REAL300025581013 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581013 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581013/0 /scratch/stefan/7787361/working/building/REAL300025581013 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/515 `/scratch/stefan/7787361/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(I)C([O-])=C1) `REAL300025581013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581013 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(I)C([O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 18, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 32, 41, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 1, 1, 7, 32, 32, 41, 41, 1, 1] 78 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581013 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(I)C([O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 18, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 3, 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: [48, 48, 24, 8, 1, 1, 1, 1, 1, 1, 1, 48, 78, 78, 78, 78, 78, 78, 78, 47, 24, 24, 8, 8, 78, 78] 78 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581013 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581013/1 /scratch/stefan/7787361/working/building/REAL300025581013 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/516 `/scratch/stefan/7787361/working/3D/516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(I)C(O)=C1) `REAL300025581013.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581013 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(I)C(O)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 18, 1, 12, 1, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [5, 1, 5, 5, 31, 48, 97, 97, 97, 97, 97, 1, 1, 1, 1, 1, 1, 1, 1, 5, 31, 31, 48, 48, 1, 2, 1] 194 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 25]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581013 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(I)C(O)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 18, 1, 12, 1, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [42, 42, 19, 7, 1, 1, 1, 1, 1, 1, 1, 42, 97, 97, 97, 97, 97, 97, 97, 42, 20, 20, 7, 7, 97, 194, 97] 194 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581013 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581013 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581013/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581013/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581013 Building REAL300025581014 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581014' /scratch/stefan/7787361/working/building/REAL300025581014 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581014 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581014/0 /scratch/stefan/7787361/working/building/REAL300025581014 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/517 `/scratch/stefan/7787361/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1[C@H](CCC(=O)NCCC2=NC(=O)O[N-]2)COC1(C)C) `REAL300025581014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581014 none CC(C)(C)OC(=O)N1[C@H](CCC(=O)NCCC2=NC(=O)O[N-]2)COC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 184, 157, 184, 157, 127, 157, 103, 38, 38, 38, 9, 9, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 130, 130, 106, 106, 38, 9, 9, 9, 9, 157, 157, 157, 157, 157, 157, 157, 157] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 781 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581014 none CC(C)(C)OC(=O)N1[C@H](CCC(=O)NCCC2=NC(=O)O[N-]2)COC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 7, 7, 4, 1, 4, 1, 1, 1, 1, 4, 6, 26, 26, 26, 66, 66, 157, 157, 157, 157, 157, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 6, 6, 26, 66, 66, 66, 66, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [5, 7, 8, 9, 10, 46, 47, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581014 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581014 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581014/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581014 Building REAL300025581015 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581015' /scratch/stefan/7787361/working/building/REAL300025581015 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581015 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581015/0 /scratch/stefan/7787361/working/building/REAL300025581015 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/518 `/scratch/stefan/7787361/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NCCC1=NC(=O)O[N-]1)N1C=C(Br)C=N1) `REAL300025581015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581015 none CC(CC(=O)NCCC1=NC(=O)O[N-]1)N1C=C(Br)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 18, 48, 48, 48, 118, 120, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 18, 18, 48, 118, 118, 120, 120, 1, 1] 201 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 618 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581015 none CC(CC(=O)NCCC1=NC(=O)O[N-]1)N1C=C(Br)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 155, 54, 54, 54, 17, 8, 1, 1, 1, 1, 1, 1, 1, 174, 201, 201, 201, 201, 201, 174, 174, 174, 174, 155, 155, 54, 17, 17, 8, 8, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 768 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581015 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581015 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581015/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581015 Building REAL300025581016 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581016' /scratch/stefan/7787361/working/building/REAL300025581016 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581016 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581016/0 /scratch/stefan/7787361/working/building/REAL300025581016 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/519 `/scratch/stefan/7787361/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2C=C(Br)C=CC2=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581016 none CN1N=C2C=C(Br)C=CC2=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 92, 92, 92, 22, 8, 1, 1, 1, 1, 1, 1, 1, 189, 189, 189, 189, 189, 189, 91, 23, 22, 8, 8] 189 rigid atoms, others: [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]) total number of confs: 433 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581016 none CN1N=C2C=C(Br)C=CC2=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 62, 83, 189, 189, 189, 189, 189, 2, 2, 2, 1, 1, 1, 12, 62, 62, 83, 83] 189 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 496 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581016 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581016 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581016/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581016 Building REAL300025581017 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581017' /scratch/stefan/7787361/working/building/REAL300025581017 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581017 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581017/0 /scratch/stefan/7787361/working/building/REAL300025581017 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/520 `/scratch/stefan/7787361/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC2=CC(Cl)=CN=C12) `REAL300025581017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581017 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC2=CC(Cl)=CN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 16, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [12, 1, 12, 12, 54, 72, 165, 165, 165, 165, 165, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 54, 54, 72, 72, 1, 1, 1] 165 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581017 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC2=CC(Cl)=CN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 16, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [71, 71, 23, 8, 1, 1, 1, 1, 1, 1, 1, 71, 165, 165, 165, 165, 165, 165, 165, 165, 165, 71, 23, 23, 8, 8, 165, 165, 165] 165 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 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/7787361/working/building/REAL300025581017 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581017 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581017/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581017 Building REAL300025581018 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581018' /scratch/stefan/7787361/working/building/REAL300025581018 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581018 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581018/0 /scratch/stefan/7787361/working/building/REAL300025581018 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/521 `/scratch/stefan/7787361/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2=CC=CC=C2C(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581018 none CC(C)(C)OC(=O)N1CC2=CC=CC=C2C(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 105, 63, 105, 63, 63, 63, 63, 63, 63, 63, 63, 35, 35, 35, 15, 8, 1, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 63, 63, 63, 63, 63, 63, 63, 35, 15, 15, 8, 8, 63, 63] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 532 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581018 none CC(C)(C)OC(=O)N1CC2=CC=CC=C2C(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 30, 63, 63, 63, 63, 63, 1, 9, 9, 9, 8, 8, 8, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 23, 23, 30, 30, 1, 1] 201 rigid atoms, others: [43, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 50, 41, 39, 49, 27, 42, 5] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581018 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581018 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581018/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581018 Building REAL300025581019 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581019' /scratch/stefan/7787361/working/building/REAL300025581019 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581019 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581019/0 /scratch/stefan/7787361/working/building/REAL300025581019 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/522 `/scratch/stefan/7787361/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025581019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581019 none CC(C)(C)OC(=O)N1CCCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 156, 128, 156, 128, 128, 128, 128, 50, 50, 50, 19, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 128, 128, 128, 128, 128, 50, 19, 19, 8, 8, 128, 128, 128, 128] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 582 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581019 none CC(C)(C)OC(=O)N1CCCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 9, 9, 46, 51, 128, 128, 128, 128, 128, 1, 1, 9, 9, 9, 9, 8, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 46, 46, 51, 51, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 46, 47, 48, 40, 23, 24, 39, 49, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581019 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581019 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581019/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581019 Building REAL300025581020 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581020' /scratch/stefan/7787361/working/building/REAL300025581020 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581020 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581020/0 /scratch/stefan/7787361/working/building/REAL300025581020 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/523 `/scratch/stefan/7787361/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CC=C1OC(F)F) `REAL300025581020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581020 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 7, 7, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 7, 7, 7, 7, 1, 1, 1, 15] 21 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581020 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [15, 15, 11, 7, 1, 1, 1, 1, 1, 1, 1, 15, 17, 17, 17, 17, 17, 17, 17, 17, 21, 21, 15, 11, 11, 7, 7, 17, 17, 17, 21] 21 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581020 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581020 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581020/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581020 Building REAL300025581021 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581021' /scratch/stefan/7787361/working/building/REAL300025581021 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581021 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581021/0 /scratch/stefan/7787361/working/building/REAL300025581021 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/524 `/scratch/stefan/7787361/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=C(Cl)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581021 none COC1=CC(Br)=C(Cl)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 16, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 189, 189, 189, 189, 189, 189, 189, 65, 65, 65, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 189, 189, 64, 20, 20, 8, 8] 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]) total number of confs: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581021 none COC1=CC(Br)=C(Cl)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 16, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 68, 80, 189, 189, 189, 189, 189, 4, 4, 4, 1, 1, 12, 68, 68, 80, 80] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581021 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581021 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581021/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581021 Building REAL300025581022 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581022' /scratch/stefan/7787361/working/building/REAL300025581022 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581022 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581022/0 /scratch/stefan/7787361/working/building/REAL300025581022 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/525 `/scratch/stefan/7787361/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C[N-]C2=C(F)C(F)=CC=C2C1=O) `REAL300025581022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581022 none O=C(NCCC1=NC(=O)O[N-]1)C1=C[N-]C2=C(F)C(F)=CC=C2C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 15, 1, 15, 1, 1, 1, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [12, 1, 12, 12, 40, 42, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 40, 40, 42, 42, 1, 1, 1] 64 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581022 none O=C(NCCC1=NC(=O)O[N-]1)C1=C[N-]C2=C(F)C(F)=CC=C2C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 15, 1, 15, 1, 1, 1, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [42, 42, 16, 8, 1, 1, 1, 1, 1, 1, 1, 42, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 41, 16, 17, 8, 8, 64, 64, 64] 64 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581022 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581022/1 /scratch/stefan/7787361/working/building/REAL300025581022 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/526 `/scratch/stefan/7787361/working/3D/526' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CNC2=C(F)C(F)=CC=C2C1=O) `REAL300025581022.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581022 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNC2=C(F)C(F)=CC=C2C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 15, 1, 15, 1, 1, 1, 1, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [13, 1, 13, 13, 75, 114, 176, 176, 176, 176, 176, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 75, 75, 114, 114, 1, 1, 1, 1] 176 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28]) total number of confs: 582 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581022 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNC2=C(F)C(F)=CC=C2C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 15, 1, 15, 1, 1, 1, 1, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [115, 115, 24, 8, 1, 1, 1, 1, 1, 1, 1, 115, 176, 176, 176, 176, 176, 176, 176, 176, 176, 176, 176, 176, 115, 25, 25, 8, 8, 176, 176, 176, 176] 176 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581022 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581022 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581022/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581022/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581022 Building REAL300025581023 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581023' /scratch/stefan/7787361/working/building/REAL300025581023 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581023 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581023/0 /scratch/stefan/7787361/working/building/REAL300025581023 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/527 `/scratch/stefan/7787361/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=C(F)C=C2)N=C1) `REAL300025581023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581023 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=C(F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 4, 13, 13, 50, 73, 129, 129, 129, 129, 129, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 50, 50, 73, 73, 4, 1, 1, 1, 1, 4] 129 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 387 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581023 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=C(F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 29, 53, 129, 129, 129, 129, 129, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 1, 5, 29, 29, 53, 53, 1, 4, 4, 4, 4, 1] 129 rigid atoms, others: [1, 33, 11, 12, 13, 14, 21, 22, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581023 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(C2=CC=C(F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 24, 8, 1, 1, 1, 1, 1, 1, 1, 71, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 70, 24, 24, 8, 8, 129, 129, 129, 129, 129, 129] 129 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581023 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581023 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581023/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581023 Building REAL300025581024 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581024' /scratch/stefan/7787361/working/building/REAL300025581024 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581024 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581024/0 /scratch/stefan/7787361/working/building/REAL300025581024 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/528 `/scratch/stefan/7787361/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C[N-]C2=C(F)C=CC(F)=C2C1=O) `REAL300025581024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581024 none O=C(NCCC1=NC(=O)O[N-]1)C1=C[N-]C2=C(F)C=CC(F)=C2C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 15, 1, 1, 1, 15, 1, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [11, 1, 11, 11, 33, 33, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 33, 33, 33, 33, 1, 1, 1] 48 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28]) total number of confs: 138 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581024 none O=C(NCCC1=NC(=O)O[N-]1)C1=C[N-]C2=C(F)C=CC(F)=C2C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 15, 1, 1, 1, 15, 1, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [32, 32, 10, 8, 1, 1, 1, 1, 1, 1, 1, 32, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 31, 10, 10, 8, 8, 48, 48, 48] 48 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581024 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581024 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581024/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581024 Building REAL300025581025 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581025' /scratch/stefan/7787361/working/building/REAL300025581025 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581025 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581025/0 /scratch/stefan/7787361/working/building/REAL300025581025 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/529 `/scratch/stefan/7787361/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CC(CC(F)(F)F)=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581025 none O=C(CC1=CC=CC(CC(F)(F)F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 88, 133, 157, 99, 157, 157, 201, 201, 201, 201, 157, 15, 7, 1, 1, 1, 1, 1, 1, 1, 88, 88, 157, 157, 145, 201, 201, 157, 37, 15, 15, 7, 7] 201 rigid atoms, others: [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: 1063 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581025 none O=C(CC1=CC=CC(CC(F)(F)F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 11, 11, 63, 70, 157, 157, 157, 157, 157, 4, 4, 1, 1, 1, 2, 2, 1, 11, 63, 63, 70, 70] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 13, 25, 26, 27, 30] set([0, 1, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581025 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581025 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581025/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581025 Building REAL300025581026 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581026' /scratch/stefan/7787361/working/building/REAL300025581026 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581026 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581026/0 /scratch/stefan/7787361/working/building/REAL300025581026 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/530 `/scratch/stefan/7787361/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1) `REAL300025581026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581026 none CC(C)(C)OC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 137, 90, 137, 90, 90, 90, 67, 67, 67, 22, 8, 1, 1, 1, 1, 1, 1, 1, 90, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 90, 67, 22, 22, 8, 8, 90] 201 rigid atoms, others: [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: 534 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581026 none CC(C)(C)OC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 20, 19, 10, 1, 10, 1, 1, 1, 1, 1, 5, 5, 6, 23, 35, 90, 90, 90, 90, 90, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 6, 23, 23, 35, 35, 1] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 40, 22, 23] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581026 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581026 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581026/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581026 Building REAL300025581027 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581027' /scratch/stefan/7787361/working/building/REAL300025581027 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581027 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581027/0 /scratch/stefan/7787361/working/building/REAL300025581027 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/531 `/scratch/stefan/7787361/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Cl)C=C2F)C2=C1CCC2) `REAL300025581027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581027 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Cl)C=C2F)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 15, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 23, 23, 85, 111, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 23, 85, 85, 111, 111, 1, 1, 1, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38, 39, 40]) total number of confs: 605 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581027 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Cl)C=C2F)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 15, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 28, 45, 124, 124, 124, 124, 124, 1, 1, 1, 1, 8, 8, 1, 7, 8, 8, 8, 1, 1, 1, 1, 1, 9, 28, 28, 45, 45, 8, 8, 8, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581027 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Cl)C=C2F)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 15, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 24, 8, 1, 1, 1, 1, 1, 1, 1, 69, 124, 124, 124, 201, 201, 143, 201, 201, 201, 201, 124, 124, 124, 124, 124, 69, 24, 24, 8, 8, 201, 201, 201, 124, 124, 124, 124, 124, 124] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 648 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581027 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581027 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581027/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581027 Building REAL300025581028 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581028' /scratch/stefan/7787361/working/building/REAL300025581028 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581028 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581028/0 /scratch/stefan/7787361/working/building/REAL300025581028 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/532 `/scratch/stefan/7787361/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Cl)C(F)=C2)C2=C1CCC2) `REAL300025581028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581028 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Cl)C(F)=C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 24, 24, 78, 97, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 24, 78, 78, 97, 97, 1, 1, 1, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38, 39, 40]) total number of confs: 558 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581028 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Cl)C(F)=C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 24, 39, 123, 123, 123, 123, 123, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 1, 1, 1, 1, 1, 6, 24, 24, 39, 39, 7, 7, 7, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 288 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581028 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Cl)C(F)=C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 24, 8, 1, 1, 1, 1, 1, 1, 1, 75, 123, 123, 123, 201, 201, 201, 201, 201, 201, 201, 123, 123, 123, 123, 123, 75, 24, 24, 8, 8, 197, 201, 201, 123, 123, 123, 123, 123, 123] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581028 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581028 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581028/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581028 Building REAL300025581029 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581029' /scratch/stefan/7787361/working/building/REAL300025581029 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581029 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581029/0 /scratch/stefan/7787361/working/building/REAL300025581029 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/533 `/scratch/stefan/7787361/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC(F)=CC(F)=C2)C2=C1CCC2) `REAL300025581029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581029 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC(F)=CC(F)=C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 8, 27, 27, 89, 111, 201, 201, 201, 199, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 27, 89, 89, 111, 111, 1, 1, 1, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38, 39, 40]) total number of confs: 598 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581029 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC(F)=CC(F)=C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 45, 62, 188, 188, 188, 188, 188, 1, 1, 1, 1, 4, 4, 4, 2, 4, 4, 4, 1, 1, 1, 1, 1, 10, 45, 45, 62, 62, 4, 4, 4, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 430 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581029 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC(F)=CC(F)=C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 24, 8, 1, 1, 1, 1, 1, 1, 1, 90, 188, 188, 188, 201, 201, 201, 201, 201, 201, 201, 188, 188, 188, 188, 188, 90, 24, 24, 8, 8, 201, 201, 201, 188, 188, 188, 188, 188, 188] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581029 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581029 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581029/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581029 Building REAL300025581030 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581030' /scratch/stefan/7787361/working/building/REAL300025581030 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581030 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581030/0 /scratch/stefan/7787361/working/building/REAL300025581030 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/534 `/scratch/stefan/7787361/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC(Cl)=CC=C2F)C2=C1CCC2) `REAL300025581030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581030 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC(Cl)=CC=C2F)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 15, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 21, 21, 79, 105, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 21, 79, 79, 105, 105, 1, 1, 1, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38, 39, 40]) total number of confs: 594 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581030 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC(Cl)=CC=C2F)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 15, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 25, 36, 116, 116, 116, 116, 116, 1, 1, 1, 1, 8, 8, 8, 3, 8, 8, 8, 1, 1, 1, 1, 1, 8, 25, 25, 36, 36, 8, 3, 8, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581030 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC(Cl)=CC=C2F)C2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 15, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 24, 8, 1, 1, 1, 1, 1, 1, 1, 66, 116, 116, 116, 201, 201, 201, 201, 201, 201, 201, 116, 116, 116, 116, 116, 66, 24, 24, 8, 8, 201, 201, 201, 116, 116, 116, 116, 116, 116] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581030 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581030 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581030/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581030 Building REAL300025581031 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581031' /scratch/stefan/7787361/working/building/REAL300025581031 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581031 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581031/0 /scratch/stefan/7787361/working/building/REAL300025581031 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/535 `/scratch/stefan/7787361/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC(Cl)=C2S1) `REAL300025581031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581031 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC(Cl)=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 1, 13, 13, 69, 99, 172, 172, 172, 172, 172, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 69, 69, 99, 99, 1, 1, 1, 1] 172 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 535 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581031 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC(Cl)=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [96, 96, 24, 8, 1, 1, 1, 1, 1, 1, 1, 96, 172, 172, 172, 172, 172, 172, 172, 172, 172, 95, 24, 24, 8, 8, 172, 172, 172, 172] 172 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581031 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581031 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581031/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581031 Building REAL300025581032 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581032' /scratch/stefan/7787361/working/building/REAL300025581032 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581032 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581032/0 /scratch/stefan/7787361/working/building/REAL300025581032 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/536 `/scratch/stefan/7787361/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CC(Br)=CC=C21) `REAL300025581032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581032 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CC(Br)=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 63, 90, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 63, 63, 90, 90, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 541 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581032 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CC(Br)=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 1, 1, 1, 1, 1, 1, 1, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 21, 21, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 594 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581032 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581032 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581032/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581032 Building REAL300025581033 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581033' /scratch/stefan/7787361/working/building/REAL300025581033 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581033 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581033/0 /scratch/stefan/7787361/working/building/REAL300025581033 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/537 `/scratch/stefan/7787361/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC([N+](=O)[O-])=C1[O-]) `REAL300025581033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581033 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC([N+](=O)[O-])=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 12, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 14, 14, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 14, 1, 1] 27 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581033 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC([N+](=O)[O-])=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 12, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 27, 27] 27 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581033 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581033 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581033/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581033 Building REAL300025581034 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581034' /scratch/stefan/7787361/working/building/REAL300025581034 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581034 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581034/0 /scratch/stefan/7787361/working/building/REAL300025581034 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/538 `/scratch/stefan/7787361/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Br)C=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581034 none COC1=C(Br)C=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 194, 194, 194, 115, 194, 194, 194, 57, 57, 57, 21, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 194, 194, 57, 21, 21, 8, 8] 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]) total number of confs: 652 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581034 none COC1=C(Br)C=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 67, 89, 194, 194, 194, 194, 194, 3, 3, 3, 1, 1, 12, 66, 66, 89, 89] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 516 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581034 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581034 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581034/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581034 Building REAL300025581035 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581035' /scratch/stefan/7787361/working/building/REAL300025581035 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581035 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581035/0 /scratch/stefan/7787361/working/building/REAL300025581035 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/539 `/scratch/stefan/7787361/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C2OCCCC2=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581035 none O=C(CC1=CC=C2OCCCC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 113, 177, 201, 201, 201, 201, 201, 201, 201, 201, 16, 8, 1, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 45, 16, 16, 8, 8] 201 rigid atoms, others: [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: 669 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581035 none O=C(CC1=CC=C2OCCCC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 76, 85, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 76, 76, 85, 85] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 35, 36, 37, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 520 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581035 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581035 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581035/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581035 Building REAL300025581036 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581036' /scratch/stefan/7787361/working/building/REAL300025581036 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581036 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581036/0 /scratch/stefan/7787361/working/building/REAL300025581036 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/540 `/scratch/stefan/7787361/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(CCCC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581036 none CSC1=CC=C(CCCC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 115, 115, 115, 115, 115, 89, 73, 25, 25, 25, 11, 7, 1, 1, 1, 1, 1, 1, 1, 115, 115, 201, 201, 201, 115, 115, 115, 115, 115, 115, 73, 73, 25, 11, 11, 7, 7, 115, 115] 201 rigid atoms, others: [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: 837 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581036 none CSC1=CC=C(CCCC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 7, 27, 27, 27, 63, 63, 115, 115, 115, 115, 115, 1, 1, 3, 3, 3, 1, 1, 3, 3, 3, 3, 7, 7, 27, 63, 63, 63, 63, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 25, 26, 38] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581036 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581036 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581036/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581036 Building REAL300025581037 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581037' /scratch/stefan/7787361/working/building/REAL300025581037 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581037 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581037/0 /scratch/stefan/7787361/working/building/REAL300025581037 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/541 `/scratch/stefan/7787361/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1N=NN=C1C1=CSC=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581037 none O=C(CN1N=NN=C1C1=CSC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 8, 8, 1, 1, 1, 14, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 108, 123, 123, 123, 123, 123, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 108, 108, 201, 201, 201, 41, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 608 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581037 none O=C(CN1N=NN=C1C1=CSC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 8, 8, 1, 1, 1, 14, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 51, 51, 102, 102, 201, 201, 201, 201, 201, 21, 21, 1, 1, 1, 51, 102, 102, 102, 102] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 581 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581037 none O=C(CN1N=NN=C1C1=CSC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 8, 8, 1, 1, 1, 14, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 22, 22, 57, 58, 123, 123, 123, 123, 123, 6, 6, 7, 7, 7, 22, 57, 57, 58, 58] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 343 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581037 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581037 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581037/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581037 Building REAL300025581038 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581038' /scratch/stefan/7787361/working/building/REAL300025581038 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581038 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581038/0 /scratch/stefan/7787361/working/building/REAL300025581038 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/542 `/scratch/stefan/7787361/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C1=CC=C(F)C(F)=C1) `REAL300025581038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581038 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 31, 31, 31, 90, 106, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 31, 90, 90, 106, 106, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 602 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581038 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 44, 44, 44, 17, 7, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 201, 201, 201, 201, 201, 201, 201, 71, 71, 71, 44, 17, 17, 7, 7, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581038 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 10, 30, 34, 71, 71, 71, 71, 71, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 10, 30, 30, 34, 34, 5, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17] set([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, 34, 35]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581038 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581038 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581038/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581038 Building REAL300025581039 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581039' /scratch/stefan/7787361/working/building/REAL300025581039 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581039 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581039/0 /scratch/stefan/7787361/working/building/REAL300025581039 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/543 `/scratch/stefan/7787361/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C(Cl)C=C2C=C1) `REAL300025581039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581039 none CC1=NC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C(Cl)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 178, 98, 98, 98, 24, 8, 1, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 98, 25, 25, 8, 8, 178, 178, 178, 178] 178 rigid atoms, others: [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]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581039 none CC1=NC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C(Cl)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 68, 94, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 68, 68, 94, 94, 1, 1, 1, 1] 178 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 34, 16, 17, 18, 19, 20, 21, 22, 33, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 530 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581039 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581039 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581039/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581039 Building REAL300025581040 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581040' /scratch/stefan/7787361/working/building/REAL300025581040 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581040 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581040/0 /scratch/stefan/7787361/working/building/REAL300025581040 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/544 `/scratch/stefan/7787361/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025581040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581040 none CCOC(=O)C1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 193, 74, 193, 74, 74, 74, 51, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 74, 74, 201, 201, 201, 201, 201, 74, 74, 74, 74, 74, 74, 51, 51, 13, 13, 13, 7, 7, 74, 74, 74, 74] 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, 41, 42, 43, 44]) total number of confs: 669 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581040 none CCOC(=O)C1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 10, 1, 10, 1, 1, 1, 1, 1, 5, 13, 13, 13, 19, 19, 74, 74, 74, 74, 74, 1, 1, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 5, 5, 13, 19, 19, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 44, 21, 22, 41, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581040 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581040 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581040/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581040 Building REAL300025581041 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581041' /scratch/stefan/7787361/working/building/REAL300025581041 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581041 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581041/0 /scratch/stefan/7787361/working/building/REAL300025581041 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/545 `/scratch/stefan/7787361/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2F)CCC1) `REAL300025581041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581041 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 3, 19, 19, 87, 104, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 87, 87, 104, 104, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 562 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581041 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 53, 69, 147, 147, 147, 147, 147, 1, 1, 3, 3, 1, 3, 3, 3, 1, 1, 1, 11, 53, 53, 69, 69, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 33, 11, 12, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 400 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581041 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 8, 1, 1, 1, 1, 1, 1, 1, 58, 147, 201, 201, 147, 201, 201, 201, 147, 147, 147, 58, 22, 22, 8, 8, 201, 201, 201, 201, 147, 147, 147, 147, 147, 147] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 821 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581041 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581041 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581041/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581041 Building REAL300025581042 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581042' /scratch/stefan/7787361/working/building/REAL300025581042 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581042 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581042/0 /scratch/stefan/7787361/working/building/REAL300025581042 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/546 `/scratch/stefan/7787361/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=CC2=CC=C(F)C=C21)NCCC1=NC(=O)O[N-]1) `REAL300025581042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581042 none O=C(CN1C=CC2=CC=C(F)C=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 13, 7, 1, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 201, 201, 36, 13, 13, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 558 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581042 none O=C(CN1C=CC2=CC=C(F)C=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 118, 120, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 37, 118, 118, 120, 120] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28] set([0, 1, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31]) total number of confs: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581042 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581042 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581042/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581042 Building REAL300025581043 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581043' /scratch/stefan/7787361/working/building/REAL300025581043 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581043 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581043/0 /scratch/stefan/7787361/working/building/REAL300025581043 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/547 `/scratch/stefan/7787361/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C2O1) `REAL300025581043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581043 none CC1(C)CC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 106, 106, 106, 54, 54, 54, 21, 8, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 53, 21, 21, 8, 8, 106, 106] 106 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, 37]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581043 none CC1(C)CC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 35, 54, 106, 106, 106, 106, 106, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 7, 35, 35, 54, 54, 1, 1] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 36, 28, 29, 30, 37] set([32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581043 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581043 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581043/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581043 Building REAL300025581044 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581044' /scratch/stefan/7787361/working/building/REAL300025581044 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581044 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581044/0 /scratch/stefan/7787361/working/building/REAL300025581044 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/548 `/scratch/stefan/7787361/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)COCC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581044 none CC(C)(C)OC(=O)COCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 29, 49, 25, 19, 19, 19, 19, 9, 7, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 29, 29, 19, 19, 19, 9, 9, 7, 7] 49 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581044 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581044 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581044/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581044 Building REAL300025581045 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581045' /scratch/stefan/7787361/working/building/REAL300025581045 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581045 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581045/0 /scratch/stefan/7787361/working/building/REAL300025581045 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/549 `/scratch/stefan/7787361/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1N1C=NC=N1) `REAL300025581045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581045 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1N1C=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 8, 27, 27, 98, 109, 201, 201, 201, 201, 201, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 27, 98, 98, 109, 109, 8, 8, 8, 1, 1] 201 rigid atoms, others: [32, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 567 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581045 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1N1C=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 45, 56, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 9, 45, 45, 56, 56, 1, 1, 1, 8, 8] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 367 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581045 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1N1C=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 19, 8, 1, 1, 1, 1, 1, 1, 1, 53, 159, 159, 159, 73, 159, 159, 159, 201, 201, 201, 201, 53, 19, 19, 8, 8, 159, 159, 159, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 699 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581045 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581045 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581045/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581045 Building REAL300025581046 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581046' /scratch/stefan/7787361/working/building/REAL300025581046 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581046 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581046/0 /scratch/stefan/7787361/working/building/REAL300025581046 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/550 `/scratch/stefan/7787361/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)N=N1) `REAL300025581046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581046 none CC1=CC=C(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 155, 155, 155, 155, 74, 74, 74, 24, 8, 1, 1, 1, 1, 1, 1, 1, 155, 155, 201, 201, 201, 201, 201, 201, 201, 155, 155, 73, 24, 24, 8, 8, 155, 155] 201 rigid atoms, others: [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: 456 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581046 none CC1=CC=C(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 30, 58, 155, 155, 155, 155, 155, 1, 1, 6, 6, 7, 7, 7, 6, 6, 1, 1, 6, 30, 30, 58, 58, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 21, 36, 29, 30, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 400 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581046 none CC1=CC=C(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 26, 26, 26, 99, 131, 201, 201, 201, 201, 201, 6, 6, 1, 1, 2, 2, 2, 1, 1, 6, 6, 26, 99, 99, 131, 131, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 655 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581046 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581046 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581046/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581046 Building REAL300025581047 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581047' /scratch/stefan/7787361/working/building/REAL300025581047 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581047 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581047/0 /scratch/stefan/7787361/working/building/REAL300025581047 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/551 `/scratch/stefan/7787361/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(Br)C=NC=C2S1) `REAL300025581047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581047 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(Br)C=NC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 17, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [12, 1, 12, 12, 63, 86, 163, 163, 163, 164, 164, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 62, 62, 86, 86, 1, 1, 1] 164 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 476 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581047 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(Br)C=NC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 17, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [85, 85, 20, 8, 1, 1, 1, 1, 1, 1, 1, 85, 164, 164, 164, 164, 164, 164, 163, 163, 163, 84, 21, 21, 8, 8, 164, 164, 163] 164 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 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/7787361/working/building/REAL300025581047 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581047 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581047/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581047 Building REAL300025581048 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581048' /scratch/stefan/7787361/working/building/REAL300025581048 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581048 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581048/0 /scratch/stefan/7787361/working/building/REAL300025581048 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/552 `/scratch/stefan/7787361/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=C(CCCC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581048 none CCCC1=CC=C(CCCC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 139, 139, 201, 201, 139, 103, 109, 29, 29, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 133, 133, 117, 117, 28, 8, 8, 8, 8, 201, 201] 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, 41, 42, 43, 44]) total number of confs: 1414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581048 none CCCC1=CC=C(CCCC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 11, 45, 45, 45, 99, 99, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 11, 11, 45, 99, 99, 99, 99, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 44, 21, 22, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581048 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581048 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581048/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581048 Building REAL300025581049 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581049' /scratch/stefan/7787361/working/building/REAL300025581049 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581049 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581049/0 /scratch/stefan/7787361/working/building/REAL300025581049 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/553 `/scratch/stefan/7787361/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=C2)N=C1) `REAL300025581049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581049 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 24, 24, 91, 120, 201, 201, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 91, 91, 120, 120, 6, 6, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 626 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581049 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 55, 185, 185, 185, 185, 185, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 5, 29, 29, 55, 55, 1, 1, 6, 6, 1, 6, 6, 1] 201 rigid atoms, others: [1, 35, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 414 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581049 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 84, 23, 8, 1, 1, 1, 1, 1, 1, 1, 84, 185, 185, 185, 185, 201, 201, 201, 201, 201, 185, 185, 84, 23, 23, 8, 8, 185, 185, 201, 201, 201, 201, 201, 185] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 445 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581049 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581049 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581049/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581049 Building REAL300025581050 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581050' /scratch/stefan/7787361/working/building/REAL300025581050 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581050 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581050/0 /scratch/stefan/7787361/working/building/REAL300025581050 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/554 `/scratch/stefan/7787361/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1N1CCOCC1) `REAL300025581050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581050 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 11, 11, 11, 44, 63, 121, 121, 121, 121, 121, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 3, 11, 44, 44, 63, 63, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1] 121 rigid atoms, others: [35, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23, 36] 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]) total number of confs: 356 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581050 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 51, 52, 52, 21, 8, 1, 1, 1, 1, 1, 1, 1, 120, 120, 119, 120, 121, 121, 121, 121, 121, 120, 120, 120, 120, 51, 22, 22, 8, 8, 120, 120, 121, 121, 121, 121, 121, 121, 121, 121] 121 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, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 297 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581050 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 37, 55, 120, 120, 120, 120, 120, 1, 1, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 7, 37, 37, 55, 55, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3] 121 rigid atoms, others: [0, 1, 2, 3, 4, 33, 34, 15, 16, 17, 18, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 331 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581050 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581050 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581050/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581050 Building REAL300025581051 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581051' /scratch/stefan/7787361/working/building/REAL300025581051 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581051 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581051/0 /scratch/stefan/7787361/working/building/REAL300025581051 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/555 `/scratch/stefan/7787361/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581051 none CC(C)(C)OC(=O)N[C@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 173, 201, 108, 108, 108, 108, 28, 108, 28, 28, 13, 8, 1, 1, 1, 1, 1, 1, 1, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 173, 108, 108, 28, 13, 13, 8, 8, 108, 108] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 635 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581051 none CC(C)(C)OC(=O)N[C@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 6, 11, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 39, 44, 108, 108, 108, 108, 108, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 9, 39, 39, 44, 44, 1, 1] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581051 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581051 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581051/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581051 Building REAL300025581052 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581052' /scratch/stefan/7787361/working/building/REAL300025581052 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581052 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581052/0 /scratch/stefan/7787361/working/building/REAL300025581052 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/556 `/scratch/stefan/7787361/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=NC=C(C(=O)NCCC3=NC(=O)O[N-]3)N2C=C1) `REAL300025581052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581052 none COC1=CC2=NC=C(C(=O)NCCC3=NC(=O)O[N-]3)N2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 195, 195, 195, 195, 195, 73, 73, 73, 21, 8, 1, 1, 1, 1, 1, 1, 1, 195, 195, 195, 201, 201, 201, 195, 195, 72, 21, 21, 8, 8, 195, 195] 201 rigid atoms, others: [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: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581052 none COC1=CC2=NC=C(C(=O)NCCC3=NC(=O)O[N-]3)N2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 58, 69, 195, 195, 195, 195, 195, 1, 1, 1, 3, 3, 3, 1, 1, 12, 58, 58, 69, 69, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 19, 20, 21, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581052 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581052 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581052/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581052 Building REAL300025581053 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581053' /scratch/stefan/7787361/working/building/REAL300025581053 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581053 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581053/0 /scratch/stefan/7787361/working/building/REAL300025581053 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/557 `/scratch/stefan/7787361/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1COC2=CC=C(O)C=C2O1) `REAL300025581053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581053 none O=C(NCCC1=NC(=O)O[N-]1)C1COC2=CC=C(O)C=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 75, 115, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 75, 75, 115, 115, 1, 1, 1, 1, 1, 2, 1] 402 rigid atoms, others: [1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 626 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581053 none O=C(NCCC1=NC(=O)O[N-]1)C1COC2=CC=C(O)C=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 24, 8, 1, 1, 1, 1, 1, 1, 1, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 24, 24, 8, 8, 201, 201, 201, 201, 201, 402, 201] 402 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1022 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581053 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581053 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581053/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581053 Building REAL300025581054 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581054' /scratch/stefan/7787361/working/building/REAL300025581054 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581054 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581054/0 /scratch/stefan/7787361/working/building/REAL300025581054 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/558 `/scratch/stefan/7787361/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(Br)C([N+](=O)[O-])=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581054 none O=C(CC1=CC=C(Br)C([N+](=O)[O-])=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 17, 1, 8, 11, 11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 115, 201, 201, 115, 200, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 115, 115, 201, 201, 201, 53, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 895 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581054 none O=C(CC1=CC=C(Br)C([N+](=O)[O-])=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 17, 1, 8, 11, 11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 83, 91, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 17, 83, 83, 91, 91] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 12, 24, 25, 26] set([0, 1, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581054 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581054 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581054/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581054 Building REAL300025581055 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581055' /scratch/stefan/7787361/working/building/REAL300025581055 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581055 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581055/0 /scratch/stefan/7787361/working/building/REAL300025581055 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/559 `/scratch/stefan/7787361/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCCC(C2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)C1) `REAL300025581055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581055 none C[N@@H+]1CCCC(C2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 71, 71, 71, 60, 60, 60, 60, 60, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 60, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 60, 60, 60, 49, 17, 17, 8, 8, 60, 71, 71] 71 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 236 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581055 none C[N@@H+]1CCCC(C2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 12, 14, 60, 60, 60, 60, 60, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 3, 12, 12, 14, 14, 1, 7, 7] 71 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 23] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 124 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581055 none C[N@@H+]1CCCC(C2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 41, 43, 71, 71, 71, 71, 71, 7, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 41, 41, 43, 43, 7, 1, 1] 71 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 44, 34, 45, 24, 33, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 210 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581055 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581055/1 /scratch/stefan/7787361/working/building/REAL300025581055 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/560 `/scratch/stefan/7787361/working/3D/560' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCCC(C2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)C1) `REAL300025581055.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581055 none C[N@H+]1CCCC(C2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 60, 60, 51, 60, 60, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 60, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 60, 60, 60, 49, 17, 17, 8, 8, 60, 72, 72] 72 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 285 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581055 none C[N@H+]1CCCC(C2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 12, 14, 60, 60, 60, 60, 60, 1, 7, 8, 8, 8, 7, 8, 7, 8, 7, 8, 7, 1, 1, 1, 3, 12, 12, 14, 14, 1, 8, 7] 72 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 23] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 134 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581055 none C[N@H+]1CCCC(C2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 8, 13, 13, 13, 42, 44, 72, 72, 72, 72, 72, 7, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 13, 42, 42, 44, 44, 8, 1, 1] 72 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 44, 34, 45, 24, 33, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 216 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581055 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581055 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581055/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581055/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581055 Building REAL300025581056 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581056' /scratch/stefan/7787361/working/building/REAL300025581056 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581056 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581056/0 /scratch/stefan/7787361/working/building/REAL300025581056 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/561 `/scratch/stefan/7787361/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(Br)=CC=C1N1CC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581056 none N#CC1=CC(Br)=CC=C1N1CC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 105, 105, 105, 38, 38, 38, 15, 7, 1, 1, 1, 1, 1, 1, 1, 105, 201, 201, 201, 105, 105, 105, 38, 15, 15, 7, 7, 105, 105] 201 rigid atoms, others: [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]) total number of confs: 471 number of broken/clashed sets: 59 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581056 none N#CC1=CC(Br)=CC=C1N1CC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 3, 4, 4, 4, 1, 1, 1, 1, 1, 11, 11, 11, 43, 48, 105, 105, 105, 105, 105, 1, 4, 4, 4, 1, 1, 1, 11, 43, 43, 48, 48, 1, 1] 201 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 23, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 283 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581056 none N#CC1=CC(Br)=CC=C1N1CC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 28, 28, 28, 94, 100, 201, 201, 201, 201, 201, 4, 1, 1, 1, 4, 4, 4, 28, 94, 94, 100, 100, 4, 4] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 559 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581056 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581056 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581056/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581056 Building REAL300025581057 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581057' /scratch/stefan/7787361/working/building/REAL300025581057 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581057 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581057/0 /scratch/stefan/7787361/working/building/REAL300025581057 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/562 `/scratch/stefan/7787361/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C(=O)NCCC1=NC(=O)O[N-]1)C(=O)OC(C)(C)C) `REAL300025581057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581057 none CC(C)C(C(=O)NCCC1=NC(=O)O[N-]1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 116, 143, 48, 48, 48, 8, 8, 1, 1, 1, 1, 1, 1, 1, 118, 187, 187, 199, 199, 199, 199, 143, 143, 143, 143, 143, 143, 143, 118, 47, 8, 8, 8, 8, 199, 199, 199, 199, 199, 199, 199, 199, 199] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 834 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581057 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581057 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581057/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581057 Building REAL300025581058 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581058' /scratch/stefan/7787361/working/building/REAL300025581058 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581058 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581058/0 /scratch/stefan/7787361/working/building/REAL300025581058 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/563 `/scratch/stefan/7787361/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(COCC(=O)NCCC2=NC(=O)O[N-]2)OC=N1) `REAL300025581058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581058 none COC(=O)C1=C(COCC(=O)NCCC2=NC(=O)O[N-]2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 131, 107, 79, 31, 31, 31, 13, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 131, 131, 79, 79, 31, 13, 13, 7, 7, 201] 201 rigid atoms, others: [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]) total number of confs: 607 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581058 none COC(=O)C1=C(COCC(=O)NCCC2=NC(=O)O[N-]2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 5, 11, 25, 43, 43, 43, 115, 115, 201, 201, 201, 201, 201, 1, 1, 1, 4, 4, 4, 5, 5, 25, 25, 43, 115, 115, 115, 115, 1] 201 rigid atoms, others: [2, 35, 4, 5, 6, 20, 21, 22] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 648 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581058 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581058 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581058/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581058 Building REAL300025581059 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581059' /scratch/stefan/7787361/working/building/REAL300025581059 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581059 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581059/0 /scratch/stefan/7787361/working/building/REAL300025581059 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/564 `/scratch/stefan/7787361/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=[NH+]C=C2)C1) `REAL300025581059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581059 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=[NH+]C=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 4, 9, 9, 23, 23, 45, 45, 45, 45, 45, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 9, 23, 23, 23, 23, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4] 45 rigid atoms, others: [33, 34, 35, 36, 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, 37, 38]) total number of confs: 113 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: REAL300025581059 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=[NH+]C=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 6, 6, 13, 14, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 6, 13, 13, 14, 14, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1] 45 rigid atoms, others: [32, 1, 37, 38, 11, 12, 13, 14, 15, 22, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581059 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C2=CC=[NH+]C=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 35, 17, 8, 1, 1, 1, 1, 1, 1, 1, 35, 37, 37, 37, 37, 45, 45, 37, 37, 45, 45, 37, 35, 17, 17, 8, 8, 37, 37, 37, 37, 37, 45, 45, 45, 45, 37, 37] 45 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 178 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581059 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581059 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581059/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581059 Building REAL300025581060 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581060' /scratch/stefan/7787361/working/building/REAL300025581060 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581060 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581060/0 /scratch/stefan/7787361/working/building/REAL300025581060 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/565 `/scratch/stefan/7787361/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CC2=CC=CC=C2OC1=O)NCCC1=NC(=O)O[N-]1) `REAL300025581060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581060 none O=C(CN1CC2=CC=CC=C2OC1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 192, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 192, 192, 201, 201, 201, 201, 201, 201, 70, 19, 19, 8, 8] 201 rigid atoms, others: [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: 731 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581060 none O=C(CN1CC2=CC=CC=C2OC1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 94, 104, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 34, 94, 94, 104, 104] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30] set([0, 1, 34, 35, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 565 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581060 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581060 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581060/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581060 Building REAL300025581061 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581061' /scratch/stefan/7787361/working/building/REAL300025581061 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581061 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581061/0 /scratch/stefan/7787361/working/building/REAL300025581061 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/566 `/scratch/stefan/7787361/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C2=CC=CC=C2)SC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025581061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581061 none CC1=C(C2=CC=CC=C2)SC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 95, 95, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 24, 25, 8, 8, 201] 201 rigid atoms, others: [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]) total number of confs: 443 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581061 none CC1=C(C2=CC=CC=C2)SC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 36, 36, 36, 114, 131, 201, 201, 201, 201, 201, 4, 4, 4, 4, 1, 1, 1, 1, 1, 36, 114, 114, 131, 131, 4] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36]) total number of confs: 624 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581061 none CC1=C(C2=CC=CC=C2)SC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 12, 12, 12, 67, 94, 201, 201, 201, 201, 201, 1, 2, 2, 2, 4, 4, 1, 4, 4, 12, 66, 66, 94, 94, 1] 201 rigid atoms, others: [0, 1, 2, 3, 36, 9, 10, 11, 22] set([4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581061 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581061 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581061/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581061 Building REAL300025581062 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581062' /scratch/stefan/7787361/working/building/REAL300025581062 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581062 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581062/0 /scratch/stefan/7787361/working/building/REAL300025581062 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/567 `/scratch/stefan/7787361/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=C(Cl)C=CC=C1Cl)NCCC1=NC(=O)O[N-]1) `REAL300025581062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581062 none O=C(CCC1=C(Cl)C=CC=C1Cl)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 199, 199, 201, 201, 201, 201, 201, 201, 201, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 92, 24, 25, 8, 8] 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]) total number of confs: 778 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581062 none O=C(CCC1=C(Cl)C=CC=C1Cl)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 69, 97, 201, 201, 201, 201, 201, 2, 2, 1, 1, 1, 1, 1, 10, 69, 69, 97, 97] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27] set([0, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 553 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581062 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581062 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581062/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581062 Building REAL300025581063 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581063' /scratch/stefan/7787361/working/building/REAL300025581063 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581063 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581063/0 /scratch/stefan/7787361/working/building/REAL300025581063 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/568 `/scratch/stefan/7787361/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)C(C2=CC=CC=C2)=C1) `REAL300025581063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581063 none CC1=NN(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)C(C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 128, 128, 128, 62, 62, 62, 19, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 61, 19, 20, 8, 8, 128, 128, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 432 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581063 none CC1=NN(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)C(C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 27, 46, 128, 128, 128, 128, 128, 1, 1, 5, 5, 9, 9, 5, 9, 9, 5, 5, 5, 5, 1, 1, 5, 27, 27, 46, 46, 1, 1, 9, 9, 5, 9, 9, 5] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 39, 40, 19, 20] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581063 none CC1=NN(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)C(C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 1, 1, 17, 17, 17, 82, 108, 201, 201, 201, 201, 201, 5, 5, 1, 1, 4, 4, 1, 4, 4, 1, 2, 2, 2, 5, 5, 17, 82, 82, 108, 108, 5, 5, 4, 4, 1, 4, 4, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 46, 21, 22, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 620 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581063 none CC1=NN(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)C(C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 4, 24, 24, 24, 82, 108, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 24, 82, 82, 108, 108, 9, 9, 1, 1, 1, 1, 1, 4] 201 rigid atoms, others: [41, 42, 43, 44, 45, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 608 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581063 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581063 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581063/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581063 Building REAL300025581064 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581064' /scratch/stefan/7787361/working/building/REAL300025581064 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581064 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581064/0 /scratch/stefan/7787361/working/building/REAL300025581064 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/569 `/scratch/stefan/7787361/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C2=CC=CC=C2)SC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025581064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581064 none CCC1=C(C2=CC=CC=C2)SC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 111, 111, 111, 111, 119, 119, 111, 119, 119, 112, 59, 59, 59, 21, 8, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 201, 119, 119, 111, 119, 119, 58, 22, 22, 8, 8, 112] 201 rigid atoms, others: [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]) total number of confs: 864 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581064 none CCC1=C(C2=CC=CC=C2)SC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 20, 20, 20, 56, 66, 119, 119, 119, 119, 119, 4, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 20, 56, 56, 66, 66, 4] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581064 none CCC1=C(C2=CC=CC=C2)SC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 8, 8, 8, 40, 48, 112, 112, 112, 112, 112, 1, 5, 5, 5, 5, 5, 4, 4, 1, 4, 4, 8, 39, 39, 48, 48, 1] 201 rigid atoms, others: [1, 2, 3, 4, 10, 11, 12, 23, 39] set([0, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581064 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581064 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581064/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581064 Building REAL300025581065 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581065' /scratch/stefan/7787361/working/building/REAL300025581065 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581065 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581065/0 /scratch/stefan/7787361/working/building/REAL300025581065 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/570 `/scratch/stefan/7787361/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1=C(F)C=CC=C1F)NCCC1=NC(=O)O[N-]1) `REAL300025581065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581065 none O=C(CCCC1=C(F)C=CC=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 15, 1, 1, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 130, 150, 201, 201, 201, 201, 201, 201, 201, 201, 15, 7, 1, 1, 1, 1, 1, 1, 1, 130, 130, 177, 177, 201, 201, 201, 201, 201, 32, 15, 15, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 1050 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581065 none O=C(CCCC1=C(F)C=CC=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 15, 1, 1, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 8, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 105, 105, 201, 201, 201, 201, 201, 8, 8, 4, 4, 2, 2, 1, 1, 1, 30, 105, 105, 105, 105] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581065 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581065 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581065/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581065 Building REAL300025581066 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581066' /scratch/stefan/7787361/working/building/REAL300025581066 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581066 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581066/0 /scratch/stefan/7787361/working/building/REAL300025581066 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/571 `/scratch/stefan/7787361/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)NC2=C(F)C=CC=C2F)CC1) `REAL300025581066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581066 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)NC2=C(F)C=CC=C2F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 20, 20, 88, 97, 201, 201, 201, 201, 201, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 88, 88, 97, 97, 3, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 557 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581066 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)NC2=C(F)C=CC=C2F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 35, 103, 103, 103, 103, 103, 1, 1, 4, 4, 4, 7, 7, 7, 4, 7, 7, 7, 1, 1, 7, 29, 29, 35, 35, 4, 7, 4, 7, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 11, 12, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 251 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581066 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)NC2=C(F)C=CC=C2F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 8, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 1, 1, 1, 1, 1, 1, 1, 60, 103, 145, 145, 145, 201, 201, 201, 145, 201, 201, 201, 103, 103, 60, 17, 17, 7, 7, 145, 201, 153, 201, 103, 103, 103, 103] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 767 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581066 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581066 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581066/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581066 Building REAL300025581067 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581067' /scratch/stefan/7787361/working/building/REAL300025581067 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581067 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581067/0 /scratch/stefan/7787361/working/building/REAL300025581067 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/572 `/scratch/stefan/7787361/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(CC(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581067 none CC(C)(C)OC(=O)N1CCCC(CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 175, 155, 175, 155, 155, 155, 154, 114, 38, 38, 38, 8, 8, 1, 1, 1, 1, 1, 1, 1, 155, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 155, 155, 155, 155, 155, 155, 120, 120, 37, 8, 8, 8, 8, 155, 155] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 694 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581067 none CC(C)(C)OC(=O)N1CCCC(CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 29, 29, 29, 76, 76, 155, 155, 155, 155, 155, 1, 6, 6, 6, 5, 5, 5, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 29, 76, 76, 76, 76, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 48, 40, 24, 39, 49, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 426 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581067 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581067 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581067/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581067 Building REAL300025581068 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581068' /scratch/stefan/7787361/working/building/REAL300025581068 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581068 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581068/0 /scratch/stefan/7787361/working/building/REAL300025581068 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/573 `/scratch/stefan/7787361/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N(CCC(=O)NCCC1=NC(=O)O[N-]1)C1CC1) `REAL300025581068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581068 none CC(C)(C)OC(=O)N(CCC(=O)NCCC1=NC(=O)O[N-]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 7, 5, 7, 1, 5, 12, 14, 43, 43, 43, 93, 93, 167, 167, 167, 167, 167, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 14, 14, 43, 93, 93, 93, 93, 1, 1, 1, 1, 1] 201 rigid atoms, others: [7, 42, 43, 44, 45, 46, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 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]) total number of confs: 493 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581068 none CC(C)(C)OC(=O)N(CCC(=O)NCCC1=NC(=O)O[N-]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 194, 182, 151, 177, 122, 110, 32, 32, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 162, 167, 167, 194, 194, 194, 194, 194, 194, 194, 194, 194, 130, 130, 118, 118, 31, 8, 8, 8, 8, 167, 167, 167, 167, 167] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 791 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581068 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581068 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581068/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581068 Building REAL300025581069 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581069' /scratch/stefan/7787361/working/building/REAL300025581069 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581069 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581069/0 /scratch/stefan/7787361/working/building/REAL300025581069 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/574 `/scratch/stefan/7787361/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1CCCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581069 none CC(C)(C)OC(=O)NCC1CCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 26, 19, 26, 12, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 19, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7] 28 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581069 none CC(C)(C)OC(=O)NCC1CCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 16, 16, 13, 9, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4] 28 rigid atoms, others: [43, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 42] 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, 34, 35, 36, 45, 46, 47, 48, 49]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581069 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581069 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581069/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581069 Building REAL300025581070 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581070' /scratch/stefan/7787361/working/building/REAL300025581070 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581070 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581070/0 /scratch/stefan/7787361/working/building/REAL300025581070 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/575 `/scratch/stefan/7787361/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)N(C)C(=O)OC(C)(C)C) `REAL300025581070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581070 none CC(C(=O)NCCC1=NC(=O)O[N-]1)N(C)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 113, 139, 139, 164, 164, 201, 201, 201, 201, 112, 113, 113, 113, 42, 8, 8, 8, 8, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 697 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581070 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581070 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581070/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581070 Building REAL300025581071 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581071' /scratch/stefan/7787361/working/building/REAL300025581071 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581071 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581071/0 /scratch/stefan/7787361/working/building/REAL300025581071 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/576 `/scratch/stefan/7787361/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(C#N)C=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581071 none CC(CC1=CC=C(C#N)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 65, 172, 201, 201, 201, 201, 201, 201, 201, 201, 65, 65, 19, 8, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 201, 201, 201, 201, 201, 201, 65, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 849 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581071 none CC(CC1=CC=C(C#N)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 26, 26, 26, 97, 107, 201, 201, 201, 201, 201, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 26, 97, 97, 107, 107] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581071 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581071 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581071/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581071 Building REAL300025581072 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581072' /scratch/stefan/7787361/working/building/REAL300025581072 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581072 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581072/0 /scratch/stefan/7787361/working/building/REAL300025581072 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/577 `/scratch/stefan/7787361/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(=O)C2=CC=CC=C21) `REAL300025581072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581072 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(=O)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 5, 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, 77, 77, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 76, 24, 24, 8, 8, 115, 115, 115, 115] 115 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 319 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581072 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(=O)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 5, 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: [1, 1, 1, 1, 7, 7, 7, 36, 53, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 36, 36, 53, 53, 1, 1, 1, 1] 115 rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581072 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581072 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581072/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581072 Building REAL300025581073 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581073' /scratch/stefan/7787361/working/building/REAL300025581073 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581073 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581073/0 /scratch/stefan/7787361/working/building/REAL300025581073 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/578 `/scratch/stefan/7787361/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC2(CC2C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581073 none CC(C)(C)OC(=O)N1CCCC2(CC2C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 154, 110, 154, 110, 110, 110, 110, 110, 110, 64, 64, 64, 23, 8, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 110, 110, 110, 110, 110, 110, 63, 24, 24, 8, 8, 110, 110] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 630 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581073 none CC(C)(C)OC(=O)N1CCCC2(CC2C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 12, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 35, 110, 110, 110, 110, 110, 1, 13, 13, 13, 13, 12, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 50, 43, 41, 25, 49, 42, 39, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 291 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581073 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581073 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581073/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581073 Building REAL300025581074 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581074' /scratch/stefan/7787361/working/building/REAL300025581074 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581074 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581074/0 /scratch/stefan/7787361/working/building/REAL300025581074 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/579 `/scratch/stefan/7787361/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(CCCCC#N)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581074 none CC(C)(C)OC(=O)NC(CCCCC#N)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 146, 115, 146, 82, 37, 82, 134, 137, 134, 154, 154, 37, 37, 15, 8, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 146, 146, 146, 146, 146, 115, 82, 137, 137, 137, 137, 137, 137, 154, 152, 37, 15, 15, 8, 8] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 981 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581074 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581074 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581074/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581074 Building REAL300025581075 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581075' /scratch/stefan/7787361/working/building/REAL300025581075 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581075 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581075/0 /scratch/stefan/7787361/working/building/REAL300025581075 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/580 `/scratch/stefan/7787361/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581075 none CC(C)(C)OC(=O)CCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 118, 201, 86, 72, 65, 19, 19, 19, 7, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 118, 86, 86, 86, 86, 65, 65, 19, 7, 7, 5, 5] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 877 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581075 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581075 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581075/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581075 Building REAL300025581076 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581076' /scratch/stefan/7787361/working/building/REAL300025581076 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581076 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581076/0 /scratch/stefan/7787361/working/building/REAL300025581076 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/581 `/scratch/stefan/7787361/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC(=O)NC1=C(F)C=CC=C1F)NCCC1=NC(=O)O[N-]1) `REAL300025581076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581076 none O=C(CCC(=O)NC1=C(F)C=CC=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 11, 8, 1, 1, 15, 1, 1, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 126, 130, 137, 137, 137, 201, 201, 201, 150, 201, 201, 201, 20, 8, 1, 1, 1, 1, 1, 1, 1, 126, 126, 130, 130, 137, 201, 197, 201, 59, 21, 21, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 910 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581076 none O=C(CCC(=O)NC1=C(F)C=CC=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 11, 8, 1, 1, 15, 1, 1, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 87, 111, 201, 201, 201, 201, 201, 12, 12, 12, 12, 3, 1, 1, 1, 25, 87, 87, 111, 111] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 626 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581076 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581076 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581076/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581076 Building REAL300025581077 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581077' /scratch/stefan/7787361/working/building/REAL300025581077 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581077 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581077/0 /scratch/stefan/7787361/working/building/REAL300025581077 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/582 `/scratch/stefan/7787361/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=NC(C2CC2)=C1) `REAL300025581077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581077 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 11, 34, 34, 111, 116, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 34, 111, 111, 116, 116, 11, 1, 1, 1, 1, 1, 11] 201 rigid atoms, others: [16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 32]) total number of confs: 571 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581077 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 33, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 29, 29, 33, 33, 1, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 20, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581077 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 17, 8, 1, 1, 1, 1, 1, 1, 1, 54, 138, 138, 138, 138, 138, 138, 201, 201, 138, 54, 17, 17, 8, 8, 138, 201, 201, 201, 201, 201, 138] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 551 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581077 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581077 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581077/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581077 Building REAL300025581078 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581078' /scratch/stefan/7787361/working/building/REAL300025581078 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581078 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581078/0 /scratch/stefan/7787361/working/building/REAL300025581078 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/583 `/scratch/stefan/7787361/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025581078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581078 none CS(=O)(=O)N1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 201, 201, 183, 183, 183, 121, 45, 45, 45, 16, 8, 1, 1, 1, 1, 1, 1, 1, 183, 183, 201, 201, 201, 183, 183, 183, 183, 183, 121, 121, 45, 16, 16, 8, 8, 183, 183, 183, 183] 201 rigid atoms, others: [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, 40]) total number of confs: 802 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581078 none CS(=O)(=O)N1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 1, 1, 1, 1, 1, 8, 25, 25, 25, 92, 96, 183, 183, 183, 183, 183, 1, 1, 7, 7, 7, 1, 1, 1, 1, 1, 8, 8, 25, 92, 92, 96, 96, 1, 1, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 38, 39, 40, 20, 21, 25, 26, 27, 28, 29, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 550 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581078 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581078 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581078/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581078 Building REAL300025581079 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581079' /scratch/stefan/7787361/working/building/REAL300025581079 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581079 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581079/0 /scratch/stefan/7787361/working/building/REAL300025581079 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/584 `/scratch/stefan/7787361/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2CCCC(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1) `REAL300025581079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581079 none COC1=CC=C2CCCC(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [195, 163, 163, 163, 163, 163, 163, 163, 163, 94, 94, 94, 24, 8, 1, 1, 1, 1, 1, 1, 1, 163, 163, 195, 195, 195, 163, 163, 163, 163, 163, 163, 163, 163, 163, 93, 24, 24, 8, 8, 163] 195 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: 574 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581079 none COC1=CC=C2CCCC(C(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 37, 58, 163, 163, 163, 163, 163, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 37, 37, 58, 58, 1] 195 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40] set([0, 35, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25]) total number of confs: 395 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581079 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581079 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581079/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581079 Building REAL300025581080 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581080' /scratch/stefan/7787361/working/building/REAL300025581080 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581080 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581080/0 /scratch/stefan/7787361/working/building/REAL300025581080 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/585 `/scratch/stefan/7787361/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN2N=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C=C1) `REAL300025581080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581080 none COC1=CN2N=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 197, 197, 197, 196, 196, 71, 71, 71, 20, 8, 1, 1, 1, 1, 1, 1, 1, 197, 197, 197, 201, 201, 201, 197, 196, 70, 20, 20, 8, 8, 197, 197] 201 rigid atoms, others: [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: 407 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581080 none COC1=CN2N=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 56, 70, 196, 196, 196, 197, 197, 1, 1, 1, 3, 3, 3, 1, 1, 10, 55, 55, 70, 70, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 19, 20, 21, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581080 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581080 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581080/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581080 Building REAL300025581081 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581081' /scratch/stefan/7787361/working/building/REAL300025581081 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581081 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581081/0 /scratch/stefan/7787361/working/building/REAL300025581081 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/586 `/scratch/stefan/7787361/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Br)C=C2)N=C1) `REAL300025581081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581081 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Br)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [17, 3, 17, 18, 56, 67, 123, 123, 123, 123, 123, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 56, 56, 67, 67, 1, 1, 1, 1, 3] 123 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 351 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581081 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Br)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 50, 61, 123, 123, 123, 123, 123, 1, 1, 1, 1, 3, 3, 2, 2, 3, 3, 1, 1, 12, 50, 50, 61, 61, 3, 3, 3, 3, 1] 123 rigid atoms, others: [32, 1, 11, 12, 13, 14, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581081 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(Br)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 22, 8, 1, 1, 1, 1, 1, 1, 1, 79, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 79, 22, 22, 8, 8, 123, 123, 123, 123, 123] 123 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581081 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581081 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581081/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581081 Building REAL300025581082 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581082' /scratch/stefan/7787361/working/building/REAL300025581082 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581082 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581082/0 /scratch/stefan/7787361/working/building/REAL300025581082 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/587 `/scratch/stefan/7787361/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2O1) `REAL300025581082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581082 none CC1(C)CC2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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: [192, 192, 192, 192, 192, 192, 192, 192, 75, 76, 76, 22, 8, 1, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 75, 22, 22, 8, 8] 192 rigid atoms, others: [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: 406 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581082 none CC1(C)CC2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 64, 89, 192, 192, 192, 192, 192, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 12, 64, 64, 89, 89] 192 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 20, 21, 28, 29, 30, 31] set([33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27]) total number of confs: 533 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581082 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581082 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581082/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581082 Building REAL300025581083 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581083' /scratch/stefan/7787361/working/building/REAL300025581083 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581083 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581083/0 /scratch/stefan/7787361/working/building/REAL300025581083 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/588 `/scratch/stefan/7787361/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CN=C1[C@@H]1[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)CCC(=O)N1C1CC1) `REAL300025581083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581083 none CN1C=CN=C1[C@@H]1[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)CCC(=O)N1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 7, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 80, 80, 80, 54, 80, 54, 54, 22, 9, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 80, 82, 82, 82, 82, 82, 54, 22, 22, 8, 8, 80, 80, 80, 80, 80, 80, 80, 80, 80] 82 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 271 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581083 none CN1C=CN=C1[C@@H]1[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)CCC(=O)N1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 7, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 29, 40, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 7, 29, 29, 40, 40, 1, 1, 1, 1, 2, 2, 2, 2, 2] 82 rigid atoms, others: [5, 6, 7, 8, 9, 10, 39, 40, 41, 21, 22, 23, 24, 25, 26, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 240 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581083 none CN1C=CN=C1[C@@H]1[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)CCC(=O)N1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 7, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 9, 9, 31, 42, 82, 82, 82, 82, 82, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 9, 31, 31, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 248 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581083 none CN1C=CN=C1[C@@H]1[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)CCC(=O)N1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 7, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 7, 7, 7, 29, 40, 80, 80, 80, 80, 80, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 29, 29, 40, 40, 2, 2, 2, 2, 1, 1, 1, 1, 1] 82 rigid atoms, others: [43, 44, 45, 46, 47, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 235 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581083 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581083 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581083/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581083 Building REAL300025581084 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581084' /scratch/stefan/7787361/working/building/REAL300025581084 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581084 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581084/0 /scratch/stefan/7787361/working/building/REAL300025581084 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/589 `/scratch/stefan/7787361/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C21) `REAL300025581084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581084 none CN1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 144, 81, 81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 81, 25, 25, 8, 8, 144, 144, 144, 144] 144 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 463 number of broken/clashed sets: 144 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581084 none CN1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 48, 70, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 9, 48, 48, 70, 70, 1, 1, 1, 1] 144 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 37, 38, 16, 17, 18, 35, 20, 21, 25, 26, 27, 28, 29, 36] set([32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 30, 31]) total number of confs: 418 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581084 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581084 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581084/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581084 Building REAL300025581085 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581085' /scratch/stefan/7787361/working/building/REAL300025581085 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581085 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581085/0 /scratch/stefan/7787361/working/building/REAL300025581085 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/590 `/scratch/stefan/7787361/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl) `REAL300025581085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581085 none CN(C)C1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 95, 95, 95, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 24, 24, 8, 8, 201] 201 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]) total number of confs: 443 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581085 none CN(C)C1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 7, 36, 65, 201, 201, 201, 201, 201, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 7, 36, 36, 65, 65, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 33, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 472 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581085 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581085 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581085/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581085 Building REAL300025581086 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581086' /scratch/stefan/7787361/working/building/REAL300025581086 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581086 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581086/0 /scratch/stefan/7787361/working/building/REAL300025581086 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/591 `/scratch/stefan/7787361/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=CC=C1C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581086 none CC(C)OC1=CC=CC=C1C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 172, 172, 172, 142, 172, 172, 139, 38, 139, 139, 38, 38, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 172, 172, 172, 172, 37, 9, 9, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 769 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581086 none CC(C)OC1=CC=CC=C1C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 48, 48, 172, 172, 172, 172, 172, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 17, 48, 48, 48, 48] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 381 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581086 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581086 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581086/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581086 Building REAL300025581087 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581087' /scratch/stefan/7787361/working/building/REAL300025581087 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581087 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581087/0 /scratch/stefan/7787361/working/building/REAL300025581087 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/592 `/scratch/stefan/7787361/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1) `REAL300025581087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581087 none CN(C)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 4, 7, 1, 4, 12, 12, 12, 56, 83, 195, 195, 195, 195, 195, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 4, 12, 56, 56, 83, 83, 1, 1, 1, 1] 198 rigid atoms, others: [19, 34, 3, 36, 37, 15, 16, 17, 18, 35, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 537 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581087 none CN(C)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [197, 191, 197, 82, 82, 82, 24, 8, 1, 1, 1, 1, 1, 1, 1, 191, 195, 195, 195, 195, 195, 195, 197, 197, 197, 197, 197, 197, 191, 81, 24, 24, 8, 8, 195, 195, 195, 195] 198 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, 34, 35, 36, 37]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581087 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581087/1 /scratch/stefan/7787361/working/building/REAL300025581087 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/593 `/scratch/stefan/7787361/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1) `REAL300025581087.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581087 none C[NH+](C)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 3, 4, 4, 1, 3, 5, 5, 5, 20, 24, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 3, 5, 20, 20, 24, 24, 1, 1, 1, 1] 49 rigid atoms, others: [35, 4, 37, 38, 16, 17, 18, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581087 none C[NH+](C)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 42, 43, 43, 34, 34, 34, 13, 8, 1, 1, 1, 1, 1, 1, 1, 42, 49, 49, 49, 49, 49, 49, 43, 43, 43, 43, 43, 43, 42, 34, 13, 13, 8, 8, 49, 49, 49, 49] 49 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581087 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581087 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581087/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581087/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581087 Building REAL300025581088 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581088' /scratch/stefan/7787361/working/building/REAL300025581088 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581088 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581088/0 /scratch/stefan/7787361/working/building/REAL300025581088 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/594 `/scratch/stefan/7787361/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1) `REAL300025581088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581088 none CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 84, 201, 35, 35, 35, 14, 7, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 35, 14, 14, 7, 7, 84, 84, 84, 84, 84, 84] 201 rigid atoms, others: [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, 39, 40, 41]) total number of confs: 591 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581088 none CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 6, 1, 6, 1, 1, 7, 7, 7, 35, 37, 84, 84, 84, 84, 84, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 35, 35, 37, 37, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 5, 38, 7, 8, 41, 39, 40, 19, 20, 21, 37] set([0, 1, 2, 3, 4, 6, 9, 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: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581088 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581088 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581088/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581088 Building REAL300025581089 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581089' /scratch/stefan/7787361/working/building/REAL300025581089 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581089 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581089/0 /scratch/stefan/7787361/working/building/REAL300025581089 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/595 `/scratch/stefan/7787361/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C(=O)NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21) `REAL300025581089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581089 none CCN1C(=O)NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 106, 106, 106, 106, 106, 106, 106, 106, 45, 45, 45, 19, 8, 1, 1, 1, 1, 1, 1, 1, 106, 106, 201, 201, 201, 201, 201, 106, 106, 106, 45, 19, 19, 8, 8, 106] 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]) total number of confs: 830 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581089 none CCN1C(=O)NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 42, 106, 106, 106, 106, 106, 1, 1, 5, 5, 5, 4, 4, 1, 1, 1, 5, 29, 29, 42, 42, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 36, 28, 29, 30] set([0, 32, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 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/7787361/working/building/REAL300025581089 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581089 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581089/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581089 Building REAL300025581090 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581090' /scratch/stefan/7787361/working/building/REAL300025581090 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581090 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581090/0 /scratch/stefan/7787361/working/building/REAL300025581090 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/596 `/scratch/stefan/7787361/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC(Br)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581090 none CSC1=CC(Br)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 17, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 178, 178, 131, 178, 178, 178, 67, 67, 67, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 178, 178, 178, 67, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 606 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581090 none CSC1=CC(Br)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 17, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 41, 51, 178, 178, 178, 178, 178, 9, 9, 9, 1, 1, 1, 9, 41, 41, 51, 51] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581090 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581090 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581090/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581090 Building REAL300025581091 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581091' /scratch/stefan/7787361/working/building/REAL300025581091 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581091 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581091/0 /scratch/stefan/7787361/working/building/REAL300025581091 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/597 `/scratch/stefan/7787361/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1Br) `REAL300025581091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581091 none COC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 7, 31, 31, 31, 117, 117, 194, 194, 194, 194, 194, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 7, 31, 117, 117, 117, 117, 1, 1, 1, 1] 194 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 582 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581091 none COC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [181, 163, 58, 57, 58, 8, 8, 1, 1, 1, 1, 1, 1, 1, 166, 194, 194, 165, 194, 194, 194, 181, 181, 181, 166, 57, 8, 8, 8, 8, 194, 194, 170, 194] 194 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 771 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581091 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581091 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581091/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581091 Building REAL300025581092 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581092' /scratch/stefan/7787361/working/building/REAL300025581092 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581092 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581092/0 /scratch/stefan/7787361/working/building/REAL300025581092 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/598 `/scratch/stefan/7787361/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)C=C1C) `REAL300025581092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581092 none CC1=CC=C(C2=NC=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 174, 174, 174, 174, 79, 79, 79, 23, 8, 1, 1, 1, 1, 1, 1, 1, 174, 201, 201, 201, 201, 201, 201, 201, 201, 174, 79, 23, 23, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [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: 447 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581092 none CC1=CC=C(C2=NC=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 5, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 52, 67, 174, 174, 174, 174, 174, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 10, 52, 52, 67, 67, 5, 5, 5, 5] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 438 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581092 none CC1=CC=C(C2=NC=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 35, 36, 36, 113, 126, 201, 201, 201, 201, 201, 5, 1, 1, 1, 2, 2, 2, 1, 1, 5, 36, 113, 113, 126, 126, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 613 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581092 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581092 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581092/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581092 Building REAL300025581093 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581093' /scratch/stefan/7787361/working/building/REAL300025581093 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581093 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581093/0 /scratch/stefan/7787361/working/building/REAL300025581093 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/599 `/scratch/stefan/7787361/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=C2OC(F)(F)OC2=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581093 none O=C(CCC1=CC=C2OC(F)(F)OC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 142, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 142, 142, 149, 149, 201, 201, 201, 41, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 705 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581093 none O=C(CCC1=CC=C2OC(F)(F)OC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 114, 116, 201, 201, 201, 201, 201, 6, 6, 2, 2, 1, 1, 1, 29, 115, 115, 116, 116] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 35, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581093 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581093 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581093/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581093 Building REAL300025581094 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581094' /scratch/stefan/7787361/working/building/REAL300025581094 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581094 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581094/0 /scratch/stefan/7787361/working/building/REAL300025581094 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/600 `/scratch/stefan/7787361/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)F)N(C2=CC=CC=C2)N=N1) `REAL300025581094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581094 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)F)N(C2=CC=CC=C2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 6, 23, 23, 71, 86, 195, 195, 195, 195, 195, 6, 6, 6, 15, 15, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 71, 71, 86, 86, 15, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 20, 21, 22, 31] 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]) total number of confs: 538 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581094 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)F)N(C2=CC=CC=C2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 28, 38, 130, 130, 130, 130, 130, 1, 1, 1, 8, 8, 1, 1, 6, 6, 1, 6, 6, 1, 1, 5, 28, 28, 38, 38, 8, 6, 6, 1, 6, 6] 201 rigid atoms, others: [1, 11, 12, 13, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581094 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)F)N(C2=CC=CC=C2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 8, 1, 1, 1, 1, 1, 1, 1, 82, 131, 131, 201, 201, 131, 131, 195, 195, 190, 195, 195, 130, 130, 81, 20, 20, 8, 8, 201, 195, 195, 131, 195, 195] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 942 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581094 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581094 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581094/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581094 Building REAL300025581095 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581095' /scratch/stefan/7787361/working/building/REAL300025581095 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581095 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581095/0 /scratch/stefan/7787361/working/building/REAL300025581095 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/601 `/scratch/stefan/7787361/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC2(CC2(F)F)CC1) `REAL300025581095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581095 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2(CC2(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 33, 51, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 33, 33, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 111 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581095 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2(CC2(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 24, 8, 1, 1, 1, 1, 1, 1, 1, 71, 111, 111, 111, 111, 111, 111, 111, 111, 111, 71, 24, 24, 8, 8, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111] 111 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581095 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581095 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581095/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581095 Building REAL300025581096 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581096' /scratch/stefan/7787361/working/building/REAL300025581096 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581096 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581096/0 /scratch/stefan/7787361/working/building/REAL300025581096 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/602 `/scratch/stefan/7787361/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)F)C=C1F) `REAL300025581096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581096 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 15, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 42, 49, 156, 156, 156, 156, 156, 1, 1, 1, 1, 1, 12, 12, 1, 1, 1, 12, 42, 42, 49, 49, 1, 1, 12, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 19, 20, 26, 27, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 21, 22, 23, 24, 25, 28]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581096 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 15, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 1, 1, 1, 1, 1, 1, 1, 62, 156, 156, 92, 156, 201, 201, 156, 156, 156, 62, 22, 22, 8, 8, 156, 156, 201, 156] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 839 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581096 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581096 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581096/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581096 Building REAL300025581097 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581097' /scratch/stefan/7787361/working/building/REAL300025581097 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581097 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581097/0 /scratch/stefan/7787361/working/building/REAL300025581097 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/603 `/scratch/stefan/7787361/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1OCC2=CC(Cl)=CC=C21)NCCC1=NC(=O)O[N-]1) `REAL300025581097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581097 none O=C(CC1OCC2=CC(Cl)=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 1, 1, 1, 16, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 167, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 167, 167, 201, 201, 201, 201, 201, 201, 61, 19, 19, 8, 8] 201 rigid atoms, others: [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: 776 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581097 none O=C(CC1OCC2=CC(Cl)=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 1, 1, 1, 16, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 103, 111, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 33, 103, 103, 111, 111] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29] set([0, 1, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31]) total number of confs: 572 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581097 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581097 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581097/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581097 Building REAL300025581098 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581098' /scratch/stefan/7787361/working/building/REAL300025581098 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581098 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581098/0 /scratch/stefan/7787361/working/building/REAL300025581098 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/604 `/scratch/stefan/7787361/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC(F)(F)F)O1) `REAL300025581098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581098 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 30, 34, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 5, 24, 24, 24, 24, 1, 7, 30, 30, 34, 34, 1, 1, 24, 24] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 21, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581098 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 53, 108, 108, 108, 108, 133, 201, 201, 201, 201, 108, 53, 19, 19, 8, 8, 108, 108, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 649 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581098 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581098 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581098/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581098 Building REAL300025581099 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581099' /scratch/stefan/7787361/working/building/REAL300025581099 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581099 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581099/0 /scratch/stefan/7787361/working/building/REAL300025581099 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/605 `/scratch/stefan/7787361/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)C2(C(=O)NCCC3=NC(=O)O[N-]3)CCCC2)C=C1) `REAL300025581099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581099 none CC1=CC=C(S(=O)(=O)C2(C(=O)NCCC3=NC(=O)O[N-]3)CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 160, 201, 201, 76, 76, 76, 23, 8, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 201, 201, 201, 201, 201, 201, 201, 76, 23, 23, 8, 8, 160, 160, 160, 160, 160, 160, 160, 160, 201, 201] 201 rigid atoms, others: [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, 40, 41, 42, 43, 44, 45]) total number of confs: 739 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581099 none CC1=CC=C(S(=O)(=O)C2(C(=O)NCCC3=NC(=O)O[N-]3)CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 1, 6, 6, 1, 1, 7, 7, 7, 33, 49, 160, 160, 160, 160, 160, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 7, 33, 33, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [36, 5, 38, 39, 8, 9, 41, 43, 40, 20, 21, 22, 23, 42, 37] set([0, 1, 2, 3, 4, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45]) total number of confs: 365 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581099 none CC1=CC=C(S(=O)(=O)C2(C(=O)NCCC3=NC(=O)O[N-]3)CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 23, 23, 23, 78, 101, 201, 201, 201, 201, 201, 9, 9, 9, 9, 1, 1, 2, 2, 2, 1, 1, 23, 78, 78, 101, 101, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 584 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581099 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581099 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581099/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581099 Building REAL300025581100 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581100' /scratch/stefan/7787361/working/building/REAL300025581100 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581100 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581100/0 /scratch/stefan/7787361/working/building/REAL300025581100 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/606 `/scratch/stefan/7787361/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(Br)=C2)CCCCC1) `REAL300025581100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581100 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(Br)=C2)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 19, 19, 79, 94, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 19, 79, 79, 94, 94, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 539 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581100 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(Br)=C2)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 25, 52, 52, 52, 52, 52, 1, 1, 9, 9, 4, 9, 9, 9, 1, 1, 1, 1, 1, 5, 19, 19, 25, 25, 9, 9, 4, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 38, 33, 40, 41, 42, 11, 12, 19, 20, 21, 22, 23, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581100 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(Br)=C2)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 14, 7, 1, 1, 1, 1, 1, 1, 1, 28, 52, 201, 201, 201, 201, 201, 201, 52, 52, 52, 52, 52, 28, 14, 14, 7, 7, 201, 201, 201, 201, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581100 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581100 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581100/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581100 Building REAL300025581101 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581101' /scratch/stefan/7787361/working/building/REAL300025581101 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581101 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581101/0 /scratch/stefan/7787361/working/building/REAL300025581101 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/607 `/scratch/stefan/7787361/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(N2C=CN=C2)=CC=C1O) `REAL300025581101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581101 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(N2C=CN=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [29, 7, 29, 29, 95, 112, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 29, 95, 95, 112, 112, 6, 1, 1, 1, 6, 6, 12] 402 rigid atoms, others: [13, 14, 15, 16, 17, 18, 29, 30, 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, 32, 33, 34]) total number of confs: 589 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581101 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(N2C=CN=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 42, 51, 116, 116, 116, 116, 116, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 10, 42, 42, 51, 51, 1, 6, 6, 6, 1, 1, 2] 402 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 19, 20, 21, 22, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31, 34]) total number of confs: 300 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581101 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(N2C=CN=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 19, 8, 1, 1, 1, 1, 1, 1, 1, 60, 116, 116, 116, 201, 201, 201, 201, 116, 116, 116, 116, 60, 19, 19, 8, 8, 116, 201, 201, 201, 116, 116, 232] 402 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 680 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581101 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581101 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581101/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581101 Building REAL300025581102 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581102' /scratch/stefan/7787361/working/building/REAL300025581102 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581102 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581102/0 /scratch/stefan/7787361/working/building/REAL300025581102 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/608 `/scratch/stefan/7787361/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(Br)=N1) `REAL300025581102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581102 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(Br)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 17, 8, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 72, 102, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 1, 12, 71, 71, 102, 102, 1] 153 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) total number of confs: 503 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581102 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(Br)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 17, 8, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 91, 153, 153, 153, 153, 153, 91, 24, 24, 8, 8, 153] 153 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581102 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581102 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581102/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581102 Building REAL300025581103 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581103' /scratch/stefan/7787361/working/building/REAL300025581103 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581103 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581103/0 /scratch/stefan/7787361/working/building/REAL300025581103 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/609 `/scratch/stefan/7787361/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=C(Cl)C(F)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl) `REAL300025581103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581103 none NC1=C(Cl)C(F)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 16, 1, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 150, 150, 150, 150, 85, 85, 85, 24, 8, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 150, 85, 24, 24, 8, 8] 150 rigid atoms, others: [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]) total number of confs: 367 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581103 none NC1=C(Cl)C(F)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 16, 1, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 43, 71, 150, 150, 150, 150, 150, 1, 1, 2, 2, 1, 7, 43, 43, 71, 71] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 23] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581103 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581103 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581103/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581103 Building REAL300025581104 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581104' /scratch/stefan/7787361/working/building/REAL300025581104 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581104 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581104/0 /scratch/stefan/7787361/working/building/REAL300025581104 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/610 `/scratch/stefan/7787361/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C(C(=O)NCCC2=NC(=O)O[N-]2)CCC1C1CC1) `REAL300025581104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581104 none CC(C)(C)OC(=O)N1C(C(=O)NCCC2=NC(=O)O[N-]2)CCC1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 21, 22, 22, 9, 3, 9, 3, 3, 3, 11, 11, 11, 54, 54, 150, 150, 150, 150, 150, 3, 3, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 11, 54, 54, 54, 54, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [46, 47, 48, 49, 50, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 358 number of broken/clashed sets: 27 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581104 none CC(C)(C)OC(=O)N1C(C(=O)NCCC2=NC(=O)O[N-]2)CCC1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 178, 131, 178, 131, 52, 52, 52, 8, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 150, 150, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 51, 9, 9, 8, 8, 131, 131, 131, 131, 131, 150, 150, 150, 150, 150] 201 rigid atoms, others: [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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 633 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581104 none CC(C)(C)OC(=O)N1C(C(=O)NCCC2=NC(=O)O[N-]2)CCC1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 19, 19, 6, 1, 6, 1, 1, 1, 8, 8, 8, 41, 41, 131, 131, 131, 131, 131, 1, 1, 1, 1, 3, 3, 20, 20, 20, 19, 19, 19, 20, 20, 20, 1, 8, 41, 41, 41, 41, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 201 rigid atoms, others: [35, 5, 7, 8, 9, 42, 43, 44, 45, 20, 21, 22, 41, 23] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 46, 47, 48, 49, 50]) total number of confs: 311 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581104 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581104 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581104/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581104 Building REAL300025581105 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581105' /scratch/stefan/7787361/working/building/REAL300025581105 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581105 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581105/0 /scratch/stefan/7787361/working/building/REAL300025581105 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/611 `/scratch/stefan/7787361/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(Cl)C([N+](=O)[O-])=C1Cl) `REAL300025581105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581105 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(Cl)C([N+](=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 16, 1, 8, 11, 11, 1, 16, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [7, 1, 7, 7, 41, 69, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 41, 41, 69, 69, 1] 142 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 23, 24, 25, 26, 27]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581105 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(Cl)C([N+](=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 16, 1, 8, 11, 11, 1, 16, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [88, 88, 23, 8, 1, 1, 1, 1, 1, 1, 1, 88, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 88, 23, 23, 8, 8, 142] 142 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581105 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581105 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581105/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581105 Building REAL300025581106 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581106' /scratch/stefan/7787361/working/building/REAL300025581106 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581106 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581106/0 /scratch/stefan/7787361/working/building/REAL300025581106 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/612 `/scratch/stefan/7787361/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(N2CCCCC2)=N1) `REAL300025581106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581106 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(N2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 8, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 27, 27, 91, 116, 201, 201, 201, 201, 201, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 27, 91, 91, 116, 116, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581106 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(N2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 8, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 25, 45, 129, 129, 129, 129, 129, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 6, 25, 25, 45, 45, 1, 9, 9, 9, 10, 9, 9, 9, 10, 9, 9] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 21, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581106 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(N2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 8, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 24, 8, 1, 1, 1, 1, 1, 1, 1, 82, 129, 129, 129, 129, 201, 201, 201, 201, 201, 129, 82, 24, 24, 8, 8, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581106 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581106 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581106/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581106 Building REAL300025581107 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581107' /scratch/stefan/7787361/working/building/REAL300025581107 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581107 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581107/0 /scratch/stefan/7787361/working/building/REAL300025581107 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/613 `/scratch/stefan/7787361/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NOC(C2=CC=CC(O)=C2)=C1) `REAL300025581107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581107 none O=C(NCCC1=NC(=O)O[N-]1)C1=NOC(C2=CC=CC(O)=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [38, 13, 38, 37, 95, 105, 201, 201, 201, 201, 201, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 38, 95, 95, 105, 105, 1, 1, 1, 2, 1, 13] 402 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 31, 33]) total number of confs: 544 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581107 none O=C(NCCC1=NC(=O)O[N-]1)C1=NOC(C2=CC=CC(O)=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 22, 30, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 13, 1, 7, 22, 22, 30, 30, 13, 13, 12, 26, 13, 1] 402 rigid atoms, others: [1, 33, 11, 12, 13, 14, 15, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581107 none O=C(NCCC1=NC(=O)O[N-]1)C1=NOC(C2=CC=CC(O)=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 24, 8, 1, 1, 1, 1, 1, 1, 1, 63, 86, 86, 86, 86, 201, 201, 201, 200, 201, 201, 86, 62, 24, 24, 8, 8, 201, 201, 201, 402, 201, 86] 402 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 840 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581107 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581107 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581107/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581107 Building REAL300025581108 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581108' /scratch/stefan/7787361/working/building/REAL300025581108 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581108 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581108/0 /scratch/stefan/7787361/working/building/REAL300025581108 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/614 `/scratch/stefan/7787361/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NCC(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1) `REAL300025581108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581108 none NS(=O)(=O)C1=CC=C(NCC(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 124, 201, 201, 124, 124, 124, 109, 81, 31, 31, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 201, 201, 124, 124, 109, 81, 81, 30, 8, 8, 8, 8, 124] 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]) total number of confs: 819 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581108 none NS(=O)(=O)C1=CC=C(NCC(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 7, 13, 34, 35, 35, 71, 71, 124, 124, 124, 124, 124, 1, 1, 1, 5, 5, 1, 1, 7, 13, 13, 35, 71, 71, 71, 71, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 21, 22, 23, 36, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 375 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581108 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581108 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581108/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581108 Building REAL300025581109 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581109' /scratch/stefan/7787361/working/building/REAL300025581109 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581109 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581109/0 /scratch/stefan/7787361/working/building/REAL300025581109 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/615 `/scratch/stefan/7787361/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CCN1C(=O)NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21) `REAL300025581109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581109 none C[NH+](C)CCN1C(=O)NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 125, 102, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 16, 8, 1, 1, 1, 1, 1, 1, 1, 50, 50, 125, 125, 125, 125, 125, 125, 125, 125, 102, 102, 50, 50, 50, 36, 16, 16, 8, 8, 50] 125 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 536 number of broken/clashed sets: 124 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581109 none C[NH+](C)CCN1C(=O)NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 12, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 17, 50, 50, 50, 50, 50, 1, 1, 17, 17, 17, 17, 17, 17, 12, 12, 6, 6, 1, 1, 1, 3, 13, 13, 17, 17, 1] 125 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 45, 25, 39, 26, 38, 37] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 195 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581109 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581109 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581109/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581109 Building REAL300025581110 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581110' /scratch/stefan/7787361/working/building/REAL300025581110 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581110 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581110/0 /scratch/stefan/7787361/working/building/REAL300025581110 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/616 `/scratch/stefan/7787361/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(C(=O)NCCC1=NC(=O)O[N-]1)C(=O)OC(C)(C)C) `REAL300025581110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581110 none CCC(CC)(C(=O)NCCC1=NC(=O)O[N-]1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 110, 41, 110, 115, 41, 41, 17, 8, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 201, 130, 130, 130, 130, 130, 131, 131, 131, 131, 131, 41, 17, 17, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581110 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581110 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581110/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581110 Building REAL300025581111 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581111' /scratch/stefan/7787361/working/building/REAL300025581111 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581111 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581111/0 /scratch/stefan/7787361/working/building/REAL300025581111 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/617 `/scratch/stefan/7787361/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=N2)N=C1) `REAL300025581111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581111 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=N2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 3, 11, 11, 49, 66, 139, 139, 139, 139, 139, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 49, 49, 66, 66, 4, 4, 1, 1, 1, 1, 4] 139 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 397 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581111 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=N2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 31, 51, 139, 139, 139, 139, 139, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 1, 1, 5, 31, 31, 51, 51, 1, 1, 4, 4, 3, 4, 1] 139 rigid atoms, others: [1, 34, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 359 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581111 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=N2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [67, 67, 22, 8, 1, 1, 1, 1, 1, 1, 1, 67, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 66, 22, 22, 8, 8, 139, 139, 139, 139, 139, 139, 139] 139 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581111 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581111 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581111/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581111 Building REAL300025581112 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581112' /scratch/stefan/7787361/working/building/REAL300025581112 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581112 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581112/0 /scratch/stefan/7787361/working/building/REAL300025581112 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/618 `/scratch/stefan/7787361/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC=CCC1) `REAL300025581112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581112 none CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 184, 59, 184, 42, 42, 42, 17, 8, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 42, 17, 17, 8, 8, 59, 59, 59, 59, 59, 59, 59, 59] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 584 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581112 none CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 6, 1, 6, 1, 1, 3, 3, 3, 15, 21, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 15, 15, 15, 14, 14, 14, 15, 15, 15, 3, 15, 15, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 5, 38, 7, 8, 41, 42, 39, 44, 45, 40, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581112 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581112 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581112/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581112 Building REAL300025581113 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581113' /scratch/stefan/7787361/working/building/REAL300025581113 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581113 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581113/0 /scratch/stefan/7787361/working/building/REAL300025581113 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/619 `/scratch/stefan/7787361/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(OC(F)(F)F)=C2)CC1) `REAL300025581113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581113 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(OC(F)(F)F)=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 3, 10, 10, 30, 32, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 1, 3, 3, 10, 30, 30, 32, 32, 1, 1, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581113 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(OC(F)(F)F)=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 20, 22, 47, 47, 47, 47, 47, 1, 1, 3, 3, 3, 3, 3, 19, 19, 19, 19, 3, 1, 1, 6, 20, 20, 22, 22, 3, 3, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 11, 12, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 144 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581113 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(OC(F)(F)F)=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 9, 6, 1, 1, 1, 1, 1, 1, 1, 17, 47, 70, 70, 70, 70, 70, 201, 201, 201, 201, 70, 47, 47, 17, 9, 9, 6, 6, 70, 70, 70, 70, 47, 47, 47, 47] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 379 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581113 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581113 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581113/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581113 Building REAL300025581114 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581114' /scratch/stefan/7787361/working/building/REAL300025581114 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581114 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581114/0 /scratch/stefan/7787361/working/building/REAL300025581114 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/620 `/scratch/stefan/7787361/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C([NH2+]C(C)C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581114 none COC1=CC=C(C([NH2+]C(C)C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 9, 6, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [120, 113, 84, 120, 120, 84, 54, 84, 108, 108, 108, 111, 111, 54, 54, 17, 8, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 120, 120, 84, 111, 111, 111, 111, 111, 111, 111, 54, 17, 17, 8, 8, 120, 120] 134 rigid atoms, others: [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]) total number of confs: 699 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581114 none COC1=CC=C(C([NH2+]C(C)C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 9, 6, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 12, 12, 12, 14, 14, 9, 21, 21, 21, 58, 68, 120, 120, 120, 120, 120, 1, 1, 2, 2, 2, 1, 1, 9, 14, 14, 14, 14, 14, 14, 14, 21, 58, 58, 68, 68, 1, 1] 134 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 45, 24, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 396 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581114 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581114 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581114/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581114 Building REAL300025581115 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581115' /scratch/stefan/7787361/working/building/REAL300025581115 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581115 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581115/0 /scratch/stefan/7787361/working/building/REAL300025581115 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/621 `/scratch/stefan/7787361/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C2=CC=CC=C2F)=N1) `REAL300025581115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581115 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C2=CC=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 48, 48, 48, 125, 127, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 48, 125, 125, 127, 127, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 604 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581115 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C2=CC=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 42, 42, 42, 17, 7, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 201, 201, 201, 201, 201, 201, 106, 106, 106, 106, 42, 17, 17, 7, 7, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 392 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581115 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C2=CC=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 36, 40, 106, 106, 106, 106, 106, 1, 1, 1, 12, 12, 2, 12, 12, 12, 1, 2, 2, 2, 9, 36, 36, 40, 40, 12, 12, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581115 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581115 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581115/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581115 Building REAL300025581116 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581116' /scratch/stefan/7787361/working/building/REAL300025581116 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581116 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581116/0 /scratch/stefan/7787361/working/building/REAL300025581116 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/622 `/scratch/stefan/7787361/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(C#CC(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025581116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581116 none CC(C)(C)OC(=O)N1CCC(C#CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 115, 57, 115, 57, 57, 57, 57, 57, 57, 56, 57, 20, 8, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 57, 56, 57, 56, 57, 56, 20, 20, 8, 8, 57, 57, 57, 57] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 565 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581116 none CC(C)(C)OC(=O)N1CCC(C#CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 16, 19, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 56, 56, 56, 56, 56, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581116 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581116 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581116/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581116 Building REAL300025581117 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581117' /scratch/stefan/7787361/working/building/REAL300025581117 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581117 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581117/0 /scratch/stefan/7787361/working/building/REAL300025581117 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/623 `/scratch/stefan/7787361/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC(N1C=CN=C1)C(F)(F)F)NCCC1=NC(=O)O[N-]1) `REAL300025581117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581117 none O=C(CC(N1C=CN=C1)C(F)(F)F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 1, 5, 15, 15, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 3, 3, 4, 4, 4, 4, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 2, 2, 2, 2, 2] 4 rigid atoms, others: [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]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581117 none O=C(CC(N1C=CN=C1)C(F)(F)F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 1, 5, 15, 15, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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, 3, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 4, 4, 4, 4, 4] 4 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581117 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581117 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581117/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581117 Building REAL300025581118 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581118' /scratch/stefan/7787361/working/building/REAL300025581118 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581118 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581118/0 /scratch/stefan/7787361/working/building/REAL300025581118 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/624 `/scratch/stefan/7787361/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCC1C1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025581118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581118 none CN1CCCC1C1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 181, 181, 181, 151, 151, 150, 150, 88, 88, 88, 23, 8, 1, 1, 1, 1, 1, 1, 1, 151, 181, 181, 181, 181, 181, 181, 181, 181, 181, 181, 150, 87, 23, 23, 8, 8, 151] 181 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]) total number of confs: 488 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581118 none CN1CCCC1C1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 52, 76, 150, 151, 150, 151, 151, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 12, 51, 51, 76, 76, 1] 181 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 21, 38] set([0, 1, 2, 3, 4, 11, 12, 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: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581118 none CN1CCCC1C1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 19, 19, 19, 78, 102, 181, 181, 181, 181, 181, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 19, 78, 78, 102, 102, 4] 181 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 537 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581118 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581118 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581118/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581118 Building REAL300025581119 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581119' /scratch/stefan/7787361/working/building/REAL300025581119 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581119 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581119/0 /scratch/stefan/7787361/working/building/REAL300025581119 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/625 `/scratch/stefan/7787361/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=NC=N2)=N1) `REAL300025581119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581119 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=NC=N2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [13, 4, 13, 12, 37, 45, 80, 80, 80, 80, 80, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 13, 37, 37, 45, 45, 3, 4, 4, 1, 1] 80 rigid atoms, others: [15, 16, 17, 18, 19, 20, 30, 31] 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]) total number of confs: 233 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581119 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=NC=N2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [11, 1, 11, 11, 37, 45, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 11, 37, 37, 45, 45, 1, 1, 1, 4, 4] 80 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581119 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=NC=N2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 49, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 49, 17, 17, 8, 8, 80, 80, 80, 80, 80] 80 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581119 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581119 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581119/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581119 Building REAL300025581120 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581120' /scratch/stefan/7787361/working/building/REAL300025581120 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581120 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581120/0 /scratch/stefan/7787361/working/building/REAL300025581120 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/626 `/scratch/stefan/7787361/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CO1) `REAL300025581120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581120 none CS(=O)(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 157, 201, 201, 157, 157, 67, 67, 67, 19, 8, 1, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 157, 67, 19, 19, 8, 8, 157] 201 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]) total number of confs: 612 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581120 none CS(=O)(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 29, 43, 157, 157, 157, 157, 157, 1, 1, 7, 7, 7, 1, 5, 29, 29, 43, 43, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 18, 19, 23, 29] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581120 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581120 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581120/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581120 Building REAL300025581121 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581121' /scratch/stefan/7787361/working/building/REAL300025581121 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581121 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581121/0 /scratch/stefan/7787361/working/building/REAL300025581121 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/627 `/scratch/stefan/7787361/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CSC[C@H]1C1=CC=CC=C1) `REAL300025581121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581121 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CSC[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 4, 19, 19, 82, 95, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 19, 82, 82, 95, 95, 4, 4, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 530 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581121 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CSC[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 43, 53, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 9, 43, 43, 53, 53, 1, 1, 1, 1, 4, 4, 1, 4, 4] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 341 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581121 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CSC[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 24, 9, 1, 1, 1, 1, 1, 1, 1, 72, 147, 147, 147, 147, 147, 147, 147, 201, 201, 147, 201, 201, 72, 24, 24, 9, 9, 147, 147, 147, 147, 201, 201, 148, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 688 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581121 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581121 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581121/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581121 Building REAL300025581122 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581122' /scratch/stefan/7787361/working/building/REAL300025581122 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581122 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581122/0 /scratch/stefan/7787361/working/building/REAL300025581122 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/628 `/scratch/stefan/7787361/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=COC2=CC=C(Cl)C=C12) `REAL300025581122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581122 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC2=CC=C(Cl)C=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 61, 81, 200, 200, 200, 200, 200, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 61, 61, 81, 81, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 504 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581122 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC2=CC=C(Cl)C=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 8, 1, 1, 1, 1, 1, 1, 1, 77, 200, 200, 201, 201, 201, 201, 201, 201, 201, 76, 23, 22, 8, 8, 200, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581122 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581122 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581122/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581122 Building REAL300025581123 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581123' /scratch/stefan/7787361/working/building/REAL300025581123 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581123 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581123/0 /scratch/stefan/7787361/working/building/REAL300025581123 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/629 `/scratch/stefan/7787361/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2NC(=O)COC2=CC=C1) `REAL300025581123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581123 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2NC(=O)COC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 3, 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: [10, 1, 10, 10, 46, 63, 157, 157, 157, 157, 157, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 46, 46, 63, 63, 1, 1, 1, 1, 1, 1] 157 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 394 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581123 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2NC(=O)COC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 3, 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: [68, 68, 22, 8, 1, 1, 1, 1, 1, 1, 1, 68, 157, 157, 157, 157, 157, 157, 157, 157, 157, 157, 68, 23, 23, 8, 8, 157, 157, 157, 157, 157, 157] 157 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 353 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581123 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581123 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581123/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581123 Building REAL300025581124 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581124' /scratch/stefan/7787361/working/building/REAL300025581124 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581124 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581124/0 /scratch/stefan/7787361/working/building/REAL300025581124 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/630 `/scratch/stefan/7787361/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(N(CC(=O)NCCC2=NC(=O)O[N-]2)C(=O)OC(C)(C)C)=C1) `REAL300025581124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581124 none COC1=CC=CC(N(CC(=O)NCCC2=NC(=O)O[N-]2)C(=O)OC(C)(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 197, 197, 197, 137, 119, 47, 47, 47, 17, 7, 1, 1, 1, 1, 1, 1, 1, 137, 163, 163, 163, 163, 163, 163, 197, 197, 197, 197, 197, 197, 197, 119, 119, 47, 17, 17, 7, 7, 163, 163, 163, 163, 163, 163, 163, 163, 163, 197] 201 rigid atoms, others: [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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 725 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581124 none COC1=CC=CC(N(CC(=O)NCCC2=NC(=O)O[N-]2)C(=O)OC(C)(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 9, 23, 37, 37, 37, 95, 99, 197, 197, 197, 197, 197, 9, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 1, 1, 1, 23, 23, 37, 95, 95, 99, 99, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 50, 27, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 617 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581124 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581124 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581124/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581124 Building REAL300025581125 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581125' /scratch/stefan/7787361/working/building/REAL300025581125 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581125 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581125/0 /scratch/stefan/7787361/working/building/REAL300025581125 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/631 `/scratch/stefan/7787361/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025581125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581125 none CC(C)(C)OC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 144, 95, 144, 95, 95, 95, 42, 42, 42, 19, 8, 1, 1, 1, 1, 1, 1, 1, 95, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 95, 42, 19, 19, 8, 8, 95] 201 rigid atoms, others: [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: 514 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581125 none CC(C)(C)OC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 22, 24, 24, 11, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 29, 35, 95, 95, 95, 95, 95, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 5, 29, 29, 35, 35, 1] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 40, 22, 23] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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 /scratch/stefan/7787361/working/building/REAL300025581125 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581125 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581125/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581125 Building REAL300025581126 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581126' /scratch/stefan/7787361/working/building/REAL300025581126 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581126 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581126/0 /scratch/stefan/7787361/working/building/REAL300025581126 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/632 `/scratch/stefan/7787361/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)C1)OCC1=CC=CC=C1) `REAL300025581126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581126 none O=C(N[C@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)C1)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 13, 26, 26, 26, 26, 26, 65, 65, 65, 121, 121, 201, 201, 201, 201, 201, 26, 4, 1, 1, 1, 1, 1, 1, 1, 13, 26, 26, 65, 121, 121, 121, 121, 26, 26, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 647 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581126 none O=C(N[C@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)C1)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 148, 44, 44, 44, 44, 15, 44, 15, 15, 7, 5, 1, 1, 1, 1, 1, 1, 1, 44, 175, 175, 201, 201, 201, 201, 201, 201, 148, 44, 44, 15, 7, 7, 5, 5, 44, 44, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44]) total number of confs: 639 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581126 none O=C(N[C@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)C1)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 44, 44, 44, 44, 44, 1, 10, 10, 16, 26, 26, 16, 26, 26, 6, 1, 1, 8, 20, 20, 20, 20, 1, 1, 16, 16, 26, 26, 16, 26, 26] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 19, 36, 29, 30, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581126 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581126 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581126/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581126 Building REAL300025581127 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581127' /scratch/stefan/7787361/working/building/REAL300025581127 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581127 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581127/0 /scratch/stefan/7787361/working/building/REAL300025581127 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/633 `/scratch/stefan/7787361/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(F)C=C1[N+](=O)[O-])NCCC1=NC(=O)O[N-]1) `REAL300025581127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581127 none O=C(CC1=CC=C(F)C=C1[N+](=O)[O-])NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 5, 3, 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: [64, 64, 64, 183, 199, 199, 199, 199, 199, 199, 199, 199, 199, 24, 8, 1, 1, 1, 1, 1, 1, 1, 183, 183, 199, 199, 199, 63, 24, 25, 8, 8] 199 rigid atoms, others: [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]) total number of confs: 721 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581127 none O=C(CC1=CC=C(F)C=C1[N+](=O)[O-])NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 5, 3, 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: [21, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 21, 21, 71, 87, 199, 199, 199, 199, 199, 4, 4, 1, 1, 1, 21, 71, 71, 87, 87] 199 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581127 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581127 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581127/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581127 Building REAL300025581128 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581128' /scratch/stefan/7787361/working/building/REAL300025581128 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581128 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581128/0 /scratch/stefan/7787361/working/building/REAL300025581128 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/634 `/scratch/stefan/7787361/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OCC(=O)NC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581128 none CC(C)(C)OCC(=O)NC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 164, 164, 164, 138, 53, 138, 138, 53, 53, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 164, 138, 138, 138, 138, 138, 138, 53, 19, 19, 8, 8] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 867 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581128 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581128 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581128/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581128 Building REAL300025581129 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581129' /scratch/stefan/7787361/working/building/REAL300025581129 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581129 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581129/0 /scratch/stefan/7787361/working/building/REAL300025581129 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/635 `/scratch/stefan/7787361/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(COCC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL300025581129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581129 none CC(COCC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 8, 18, 38, 54, 54, 54, 128, 128, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 8, 38, 38, 54, 128, 128, 128, 128, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21] set([0, 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]) total number of confs: 668 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581129 none CC(COCC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 160, 130, 100, 37, 37, 37, 15, 7, 1, 1, 1, 1, 1, 1, 1, 200, 201, 201, 201, 201, 201, 200, 200, 200, 200, 160, 160, 100, 100, 37, 15, 15, 7, 7, 201, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 820 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581129 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581129 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581129/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581129 Building REAL300025581130 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581130' /scratch/stefan/7787361/working/building/REAL300025581130 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581130 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581130/0 /scratch/stefan/7787361/working/building/REAL300025581130 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/636 `/scratch/stefan/7787361/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCCC1=CC=CC(F)=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581130 none O=C(COCCC1=CC=CC(F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 60, 81, 105, 153, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 67, 67, 105, 105, 153, 153, 201, 201, 201, 201, 28, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581130 none O=C(COCCC1=CC=CC(F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 54, 19, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 110, 110, 201, 201, 201, 201, 201, 54, 54, 7, 7, 3, 3, 1, 1, 1, 1, 72, 110, 110, 110, 110] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 627 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581130 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581130 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581130/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581130 Building REAL300025581131 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581131' /scratch/stefan/7787361/working/building/REAL300025581131 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581131 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581131/0 /scratch/stefan/7787361/working/building/REAL300025581131 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/637 `/scratch/stefan/7787361/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CCC[C@H]1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581131 none CC(C)(C)OC(=O)N[C@@H]1CCC[C@H]1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 197, 174, 197, 142, 142, 142, 142, 142, 142, 110, 142, 41, 41, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 174, 142, 142, 142, 142, 142, 142, 117, 117, 40, 8, 8, 8, 8] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 745 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581131 none CC(C)(C)OC(=O)N[C@@H]1CCC[C@H]1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 9, 5, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 56, 56, 142, 142, 142, 142, 142, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 19, 56, 56, 56, 56] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581131 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581131 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581131/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581131 Building REAL300025581132 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581132' /scratch/stefan/7787361/working/building/REAL300025581132 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581132 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581132/0 /scratch/stefan/7787361/working/building/REAL300025581132 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/638 `/scratch/stefan/7787361/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CCC[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581132 none CC(C)(C)OC(=O)N[C@@H]1CCC[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 171, 140, 171, 107, 107, 107, 107, 107, 107, 56, 107, 56, 56, 20, 9, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 107, 107, 107, 107, 107, 107, 56, 20, 20, 9, 9] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 652 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581132 none CC(C)(C)OC(=O)N[C@@H]1CCC[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 13, 13, 7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 29, 35, 107, 107, 107, 107, 107, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 7, 29, 29, 35, 35] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46]) total number of confs: 276 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581132 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581132 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581132/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581132 Building REAL300025581133 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581133' /scratch/stefan/7787361/working/building/REAL300025581133 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581133 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581133/0 /scratch/stefan/7787361/working/building/REAL300025581133 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/639 `/scratch/stefan/7787361/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCOC2=CC=C(Br)C=C21) `REAL300025581133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581133 none O=C(NCCC1=NC(=O)O[N-]1)C1CCOC2=CC=C(Br)C=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 41, 62, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 41, 41, 62, 62, 1, 1, 1, 1, 1, 1, 1, 1] 133 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 368 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581133 none O=C(NCCC1=NC(=O)O[N-]1)C1CCOC2=CC=C(Br)C=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 22, 8, 1, 1, 1, 1, 1, 1, 1, 77, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 77, 23, 23, 8, 8, 133, 133, 133, 133, 133, 133, 133, 133] 133 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 433 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581133 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581133 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581133/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581133 Building REAL300025581134 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581134' /scratch/stefan/7787361/working/building/REAL300025581134 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581134 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581134/0 /scratch/stefan/7787361/working/building/REAL300025581134 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/640 `/scratch/stefan/7787361/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1) `REAL300025581134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581134 none CNC(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 82, 49, 115, 115, 49, 49, 49, 15, 7, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 201, 201, 201, 201, 201, 115, 115, 49, 15, 15, 7, 7, 115] 201 rigid atoms, others: [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]) total number of confs: 773 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581134 none CNC(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 31, 31, 115, 115, 115, 115, 115, 1, 1, 1, 9, 9, 9, 9, 5, 1, 1, 7, 31, 31, 31, 31, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581134 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581134 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581134/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581134 Building REAL300025581135 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581135' /scratch/stefan/7787361/working/building/REAL300025581135 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581135 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581135/0 /scratch/stefan/7787361/working/building/REAL300025581135 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/641 `/scratch/stefan/7787361/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1N=C2CCCCN2C1=O)NCCC1=NC(=O)O[N-]1) `REAL300025581135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581135 none O=C(CN1N=C2CCCCN2C1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 20, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 65, 20, 20, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 642 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581135 none O=C(CN1N=C2CCCCN2C1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 98, 111, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 35, 98, 98, 111, 111] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 35, 36, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 612 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581135 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581135 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581135/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581135 Building REAL300025581136 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581136' /scratch/stefan/7787361/working/building/REAL300025581136 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581136 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581136/0 /scratch/stefan/7787361/working/building/REAL300025581136 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/642 `/scratch/stefan/7787361/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC2=CC=NC=C21) `REAL300025581136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581136 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC2=CC=NC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 57, 87, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 57, 57, 87, 87, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 537 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581136 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC2=CC=NC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 24, 23, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581136 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581136 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581136/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581136 Building REAL300025581137 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581137' /scratch/stefan/7787361/working/building/REAL300025581137 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581137 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581137/0 /scratch/stefan/7787361/working/building/REAL300025581137 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/643 `/scratch/stefan/7787361/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C1=CC=CC(C(F)(F)F)=C1) `REAL300025581137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581137 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 19, 19, 19, 74, 99, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 19, 74, 74, 99, 99, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 573 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581137 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 61, 61, 24, 8, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 201, 201, 88, 201, 201, 201, 201, 201, 201, 88, 88, 88, 88, 61, 24, 24, 8, 8, 201, 201, 88, 201] 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, 34, 35, 36, 37, 38, 39]) total number of confs: 665 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581137 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 20, 30, 88, 88, 88, 88, 88, 1, 1, 1, 7, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 5, 20, 20, 30, 30, 7, 7, 1, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581137 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581137 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581137/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581137 Building REAL300025581138 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581138' /scratch/stefan/7787361/working/building/REAL300025581138 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581138 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581138/0 /scratch/stefan/7787361/working/building/REAL300025581138 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/644 `/scratch/stefan/7787361/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(S1)C(=O)NC=C2) `REAL300025581138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581138 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(S1)C(=O)NC=C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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: [12, 1, 12, 12, 63, 86, 150, 150, 150, 150, 150, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 62, 62, 86, 86, 1, 1, 1, 1] 150 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581138 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(S1)C(=O)NC=C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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: [86, 86, 24, 8, 1, 1, 1, 1, 1, 1, 1, 86, 150, 150, 150, 150, 150, 150, 150, 150, 150, 86, 25, 25, 8, 8, 150, 150, 150, 150] 150 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581138 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581138 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581138/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581138 Building REAL300025581139 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581139' /scratch/stefan/7787361/working/building/REAL300025581139 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581139 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581139/0 /scratch/stefan/7787361/working/building/REAL300025581139 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/645 `/scratch/stefan/7787361/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=CC=CC=C2Cl)N=C1) `REAL300025581139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581139 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=CC=CC=C2Cl)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 19, 19, 84, 115, 201, 201, 201, 201, 201, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 84, 84, 115, 115, 6, 1, 1, 1, 1, 6] 201 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 613 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581139 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=CC=CC=C2Cl)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 54, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 5, 29, 29, 54, 54, 1, 6, 6, 6, 6, 1] 201 rigid atoms, others: [1, 34, 11, 12, 13, 14, 15, 22, 23, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581139 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=CC=CC=C2Cl)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 77, 159, 159, 125, 159, 201, 201, 201, 201, 201, 201, 159, 159, 76, 24, 24, 8, 8, 159, 201, 201, 201, 201, 159] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581139 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581139 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581139/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581139 Building REAL300025581140 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581140' /scratch/stefan/7787361/working/building/REAL300025581140 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581140 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581140/0 /scratch/stefan/7787361/working/building/REAL300025581140 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/646 `/scratch/stefan/7787361/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=NN1C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581140 none CC1=NN=NN1C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 161, 161, 161, 161, 77, 77, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 161, 161, 201, 201, 201, 161, 161, 76, 24, 24, 8, 8, 161, 161] 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]) total number of confs: 459 number of broken/clashed sets: 34 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581140 none CC1=NN=NN1C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 53, 161, 161, 161, 161, 161, 1, 1, 6, 6, 6, 1, 1, 5, 29, 29, 53, 53, 1, 1] 201 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 21, 22, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 389 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581140 none CC1=NN=NN1C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 5, 5, 18, 18, 18, 84, 118, 201, 201, 201, 201, 201, 6, 6, 2, 2, 2, 6, 6, 18, 84, 84, 118, 118, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 637 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581140 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581140 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581140/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581140 Building REAL300025581141 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581141' /scratch/stefan/7787361/working/building/REAL300025581141 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581141 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581141/0 /scratch/stefan/7787361/working/building/REAL300025581141 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/647 `/scratch/stefan/7787361/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC([N+](=O)[O-])=NN1CC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025581141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581141 none CC1=CC([N+](=O)[O-])=NN1CC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 167, 86, 86, 58, 86, 86, 42, 42, 42, 17, 8, 1, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 201, 167, 167, 86, 86, 86, 42, 17, 17, 8, 8, 86] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 806 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581141 none CC1=CC([N+](=O)[O-])=NN1CC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 8, 9, 9, 9, 9, 9, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 25, 86, 86, 86, 86, 86, 1, 9, 9, 9, 9, 6, 6, 1, 1, 1, 5, 23, 23, 25, 25, 1] 201 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 41, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581141 none CC1=CC([N+](=O)[O-])=NN1CC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 27, 27, 27, 98, 106, 201, 201, 201, 201, 201, 8, 2, 2, 2, 1, 4, 4, 8, 8, 8, 27, 98, 98, 106, 106, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 585 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581141 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581141 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581141/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581141 Building REAL300025581142 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581142' /scratch/stefan/7787361/working/building/REAL300025581142 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581142 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581142/0 /scratch/stefan/7787361/working/building/REAL300025581142 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/648 `/scratch/stefan/7787361/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2CC2)C(C)=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581142 none CC1=NN(CC2CC2)C(C)=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 154, 201, 201, 87, 87, 71, 30, 30, 30, 15, 7, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 154, 154, 201, 201, 201, 201, 201, 87, 87, 87, 71, 71, 30, 15, 15, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 876 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581142 none CC1=NN(CC2CC2)C(C)=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 6, 1, 1, 1, 1, 15, 15, 15, 15, 22, 62, 62, 62, 121, 121, 201, 201, 201, 201, 201, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 15, 15, 15, 22, 22, 62, 121, 121, 121, 121] 201 rigid atoms, others: [32, 4, 5, 6, 7, 28, 29, 30, 31] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 638 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581142 none CC1=NN(CC2CC2)C(C)=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 15, 15, 1, 1, 1, 1, 2, 13, 13, 13, 40, 40, 87, 87, 87, 87, 87, 2, 2, 2, 5, 5, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 13, 40, 40, 40, 40] 201 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11] set([5, 6, 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]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581142 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581142 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581142/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581142 Building REAL300025581143 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581143' /scratch/stefan/7787361/working/building/REAL300025581143 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581143 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581143/0 /scratch/stefan/7787361/working/building/REAL300025581143 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/649 `/scratch/stefan/7787361/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=C1)C1=C(CCCC1)N2CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581143 none COC1=CC=C2C(=C1)C1=C(CCCC1)N2CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 44, 44, 44, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 44, 17, 17, 8, 8] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 676 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581143 none COC1=CC=C2C(=C1)C1=C(CCCC1)N2CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 22, 22, 22, 74, 82, 201, 201, 201, 201, 201, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 22, 74, 74, 82, 82] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581143 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581143 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581143/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581143 Building REAL300025581144 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581144' /scratch/stefan/7787361/working/building/REAL300025581144 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581144 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581144/0 /scratch/stefan/7787361/working/building/REAL300025581144 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/650 `/scratch/stefan/7787361/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1=CC=C2CCCCC2=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581144 none O=C(CCCC1=CC=C2CCCCC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 67, 75, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 7, 3, 1, 1, 1, 1, 1, 1, 1, 67, 67, 103, 103, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 15, 7, 7, 3, 3] 201 rigid atoms, others: [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]) total number of confs: 819 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581144 none O=C(CCCC1=CC=C2CCCCC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 99, 99, 201, 201, 201, 201, 201, 7, 7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 99, 99, 99, 99] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 41, 42, 43, 44, 45]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581144 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581144 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581144/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581144 Building REAL300025581145 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581145' /scratch/stefan/7787361/working/building/REAL300025581145 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581145 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581145/0 /scratch/stefan/7787361/working/building/REAL300025581145 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/651 `/scratch/stefan/7787361/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1OCCCO2) `REAL300025581145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581145 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1OCCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 12, 64, 92, 177, 177, 177, 177, 177, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 64, 64, 92, 92, 1, 1, 1, 1, 1, 1, 1, 1, 1] 177 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 525 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581145 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1OCCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [77, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 77, 177, 177, 177, 177, 177, 177, 177, 177, 177, 177, 77, 25, 25, 8, 8, 177, 177, 177, 177, 177, 177, 177, 177, 177] 177 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581145 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581145 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581145/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581145 Building REAL300025581146 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581146' /scratch/stefan/7787361/working/building/REAL300025581146 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581146 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581146/0 /scratch/stefan/7787361/working/building/REAL300025581146 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/652 `/scratch/stefan/7787361/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(N2C=NN=N2)CCCCC1) `REAL300025581146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581146 none O=C(NCCC1=NC(=O)O[N-]1)C1(N2C=NN=N2)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 8, 1, 8, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 5, 30, 30, 80, 91, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 30, 80, 80, 91, 91, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 513 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581146 none O=C(NCCC1=NC(=O)O[N-]1)C1(N2C=NN=N2)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 8, 1, 8, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 47, 61, 175, 175, 175, 175, 175, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 47, 47, 61, 61, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 11, 12, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 413 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581146 none O=C(NCCC1=NC(=O)O[N-]1)C1(N2C=NN=N2)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 8, 1, 8, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 19, 8, 1, 1, 1, 1, 1, 1, 1, 75, 175, 201, 201, 201, 201, 175, 175, 175, 175, 175, 75, 19, 19, 8, 8, 201, 175, 175, 175, 175, 175, 175, 175, 175, 175, 175] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 584 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581146 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581146 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581146/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581146 Building REAL300025581147 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581147' /scratch/stefan/7787361/working/building/REAL300025581147 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581147 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581147/0 /scratch/stefan/7787361/working/building/REAL300025581147 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/653 `/scratch/stefan/7787361/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2Cl)CCC1) `REAL300025581147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581147 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2Cl)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 21, 21, 89, 100, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 89, 89, 100, 100, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 554 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581147 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2Cl)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 54, 65, 182, 182, 182, 182, 182, 1, 1, 5, 5, 2, 5, 5, 5, 1, 1, 1, 10, 54, 54, 65, 65, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 33, 11, 12, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 418 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581147 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2Cl)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 8, 1, 1, 1, 1, 1, 1, 1, 58, 182, 201, 201, 201, 201, 201, 201, 182, 182, 182, 57, 19, 18, 8, 8, 201, 201, 201, 201, 182, 182, 182, 182, 182, 182] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 555 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581147 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581147 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581147/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581147 Building REAL300025581148 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581148' /scratch/stefan/7787361/working/building/REAL300025581148 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581148 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581148/0 /scratch/stefan/7787361/working/building/REAL300025581148 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/654 `/scratch/stefan/7787361/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NSC=C1Br) `REAL300025581148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581148 none O=C(NCCC1=NC(=O)O[N-]1)C1=NSC=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 14, 1, 1, 17, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 37, 63, 167, 167, 167, 167, 167, 1, 1, 1, 1, 1, 1, 7, 37, 37, 63, 63, 1] 167 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581148 none O=C(NCCC1=NC(=O)O[N-]1)C1=NSC=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 14, 1, 1, 17, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 24, 8, 1, 1, 1, 1, 1, 1, 1, 101, 167, 167, 167, 167, 167, 101, 24, 24, 8, 8, 167] 167 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581148 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581148 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581148/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581148 Building REAL300025581149 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581149' /scratch/stefan/7787361/working/building/REAL300025581149 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581149 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581149/0 /scratch/stefan/7787361/working/building/REAL300025581149 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/655 `/scratch/stefan/7787361/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CC(Cl)=CN2C=N1) `REAL300025581149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581149 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CC(Cl)=CN2C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 12, 67, 97, 188, 188, 188, 188, 188, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 67, 67, 97, 97, 1, 1, 1, 1] 188 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 546 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581149 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CC(Cl)=CN2C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [99, 99, 22, 8, 1, 1, 1, 1, 1, 1, 1, 99, 188, 188, 188, 188, 188, 188, 188, 188, 188, 98, 22, 22, 8, 8, 188, 188, 188, 188] 188 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 425 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581149 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581149 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581149/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581149 Building REAL300025581150 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581150' /scratch/stefan/7787361/working/building/REAL300025581150 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581150 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581150/0 /scratch/stefan/7787361/working/building/REAL300025581150 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/656 `/scratch/stefan/7787361/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(COCC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581150 none CCC(CC)(COCC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 57, 57, 57, 59, 57, 63, 111, 201, 201, 201, 201, 201, 201, 57, 57, 19, 8, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 63, 63, 201, 201, 201, 201, 201, 201, 201, 57, 19, 19, 8, 8] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 723 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581150 none CCC(CC)(COCC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 31, 33, 33, 15, 3, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 112, 119, 201, 201, 201, 201, 201, 33, 33, 33, 33, 33, 33, 33, 34, 34, 34, 31, 31, 3, 3, 1, 1, 1, 1, 1, 33, 112, 112, 118, 118] 201 rigid atoms, others: [11, 39, 8, 9, 10, 7, 12, 13, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48]) total number of confs: 615 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581150 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581150 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581150/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581150 Building REAL300025581151 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581151' /scratch/stefan/7787361/working/building/REAL300025581151 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581151 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581151/0 /scratch/stefan/7787361/working/building/REAL300025581151 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/657 `/scratch/stefan/7787361/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CCC(NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581151 none C[NH+](C)CCC(NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', '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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 43, 48, 45, 36, 39, 26, 39, 48, 54, 54, 57, 57, 57, 57, 26, 26, 12, 7, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 43, 43, 43, 43, 39, 48, 57, 57, 57, 57, 57, 57, 57, 57, 57, 26, 12, 12, 7, 7] 58 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 374 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581151 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581151 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581151/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581151 Building REAL300025581152 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581152' /scratch/stefan/7787361/working/building/REAL300025581152 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581152 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581152/0 /scratch/stefan/7787361/working/building/REAL300025581152 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/658 `/scratch/stefan/7787361/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)C=C1) `REAL300025581152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581152 none COC1=CC=C(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 156, 201, 201, 156, 62, 62, 62, 62, 32, 32, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201, 156, 156, 31, 8, 8, 8, 8, 62, 62, 62, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 863 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581152 none COC1=CC=C(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 10, 5, 18, 18, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 62, 62, 61, 62, 62, 1, 1, 18, 18, 19, 19, 19, 18, 18, 5, 5, 4, 14, 14, 14, 14, 2, 2, 2, 18, 18] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 22, 23] set([0, 1, 2, 3, 4, 5, 12, 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: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581152 none COC1=CC=C(CN2N=NC(C(=O)NCCC3=NC(=O)O[N-]3)=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 51, 51, 51, 112, 112, 201, 201, 201, 201, 201, 18, 18, 1, 1, 2, 2, 2, 1, 1, 6, 6, 51, 112, 112, 112, 112, 19, 19, 19, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 24, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 611 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581152 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581152 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581152/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581152 Building REAL300025581153 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581153' /scratch/stefan/7787361/working/building/REAL300025581153 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581153 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581153/0 /scratch/stefan/7787361/working/building/REAL300025581153 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/659 `/scratch/stefan/7787361/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(Br)=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581153 none N#CC1=CC(Br)=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 135, 34, 34, 34, 16, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 135, 135, 34, 16, 16, 8, 8] 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]) total number of confs: 625 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581153 none N#CC1=CC(Br)=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 35, 35, 35, 104, 106, 201, 201, 201, 201, 201, 1, 1, 1, 6, 6, 35, 104, 104, 106, 106] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 562 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581153 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581153 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581153/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581153 Building REAL300025581154 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581154' /scratch/stefan/7787361/working/building/REAL300025581154 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581154 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581154/0 /scratch/stefan/7787361/working/building/REAL300025581154 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/660 `/scratch/stefan/7787361/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(CC2=C(Cl)C=CC=C2Cl)S1) `REAL300025581154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581154 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(CC2=C(Cl)C=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 5, 1, 1, 16, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 11, 33, 33, 101, 106, 201, 201, 201, 201, 201, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 33, 101, 101, 106, 106, 11, 3, 3, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 566 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581154 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(CC2=C(Cl)C=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 5, 1, 1, 16, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 21, 23, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 8, 11, 11, 11, 8, 11, 11, 11, 1, 6, 20, 20, 23, 23, 1, 8, 8, 11, 8, 11] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 24, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581154 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(CC2=C(Cl)C=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 5, 1, 1, 16, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 40, 71, 71, 71, 71, 201, 201, 201, 201, 201, 201, 201, 201, 71, 40, 19, 19, 8, 8, 71, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 705 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581154 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581154 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581154/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581154 Building REAL300025581155 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581155' /scratch/stefan/7787361/working/building/REAL300025581155 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581155 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581155/0 /scratch/stefan/7787361/working/building/REAL300025581155 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/661 `/scratch/stefan/7787361/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=CC=CC(Cl)=C2)S1) `REAL300025581155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581155 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=CC=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 5, 31, 31, 94, 113, 201, 201, 201, 201, 201, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 31, 94, 94, 113, 113, 5, 1, 1, 1, 1] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 568 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581155 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=CC=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 11, 43, 61, 173, 173, 173, 173, 173, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 1, 11, 43, 43, 61, 61, 1, 5, 5, 4, 5] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 22, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 415 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581155 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=CC=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 81, 173, 173, 173, 173, 201, 201, 201, 201, 201, 201, 173, 81, 25, 25, 8, 8, 173, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581155 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581155 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581155/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581155 Building REAL300025581156 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581156' /scratch/stefan/7787361/working/building/REAL300025581156 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581156 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581156/0 /scratch/stefan/7787361/working/building/REAL300025581156 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/662 `/scratch/stefan/7787361/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=C(F)C=CC=C2F)S1) `REAL300025581156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581156 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=C(F)C=CC=C2F)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 9, 36, 36, 118, 137, 201, 201, 201, 201, 201, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 36, 118, 118, 137, 137, 9, 1, 1, 1] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 622 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581156 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=C(F)C=CC=C2F)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 35, 43, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 7, 34, 34, 43, 43, 1, 7, 7, 7] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 23, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581156 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=C(F)C=CC=C2F)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 23, 8, 1, 1, 1, 1, 1, 1, 1, 63, 127, 127, 127, 127, 201, 201, 201, 201, 201, 201, 201, 127, 63, 23, 23, 8, 8, 127, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581156 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581156 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581156/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581156 Building REAL300025581157 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581157' /scratch/stefan/7787361/working/building/REAL300025581157 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581157 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581157/0 /scratch/stefan/7787361/working/building/REAL300025581157 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/663 `/scratch/stefan/7787361/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Br) `REAL300025581157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581157 none CC(C)OC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 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, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 138, 138, 138, 48, 48, 48, 17, 8, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 201, 201, 201, 201, 201, 201, 201, 138, 48, 17, 17, 8, 8, 138, 138] 201 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: 418 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581157 none CC(C)OC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 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, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 11, 1, 1, 1, 1, 1, 5, 5, 5, 29, 33, 138, 138, 138, 138, 138, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 5, 29, 29, 33, 33, 1, 1] 201 rigid atoms, others: [35, 3, 4, 5, 6, 7, 18, 19, 20, 21, 36, 29] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 280 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581157 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581157 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581157/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581157 Building REAL300025581158 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581158' /scratch/stefan/7787361/working/building/REAL300025581158 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581158 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581158/0 /scratch/stefan/7787361/working/building/REAL300025581158 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/664 `/scratch/stefan/7787361/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1C2CC3CC(C2)CC1C3)NCCC1=NC(=O)O[N-]1) `REAL300025581158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581158 none O=C(CC1C2CC3CC(C2)CC1C3)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 178, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 178, 178, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 51, 19, 19, 8, 8] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 770 number of broken/clashed sets: 95 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581158 none O=C(CC1C2CC3CC(C2)CC1C3)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 98, 104, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 98, 98, 104, 104] 201 rigid atoms, others: [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] set([0, 1, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 528 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581158 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581158 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581158/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581158 Building REAL300025581159 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581159' /scratch/stefan/7787361/working/building/REAL300025581159 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581159 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581159/0 /scratch/stefan/7787361/working/building/REAL300025581159 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/665 `/scratch/stefan/7787361/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1(CN2C=NN=N2)CCCCC1)NCCC1=NC(=O)O[N-]1) `REAL300025581159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581159 none O=C(CC1(CN2C=NN=N2)CCCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 8, 8, 8, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 102, 152, 180, 201, 201, 201, 201, 152, 152, 152, 152, 152, 16, 8, 1, 1, 1, 1, 1, 1, 1, 102, 102, 180, 180, 201, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152, 52, 16, 16, 8, 8] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 788 number of broken/clashed sets: 50 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581159 none O=C(CC1(CN2C=NN=N2)CCCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 8, 8, 8, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 19, 11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 35, 35, 104, 112, 201, 201, 201, 201, 201, 19, 19, 5, 5, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 35, 104, 104, 112, 112] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 629 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581159 none O=C(CC1(CN2C=NN=N2)CCCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 8, 8, 8, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 6, 11, 11, 11, 11, 1, 1, 1, 1, 1, 13, 13, 62, 70, 152, 152, 152, 152, 152, 5, 5, 6, 6, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 62, 62, 70, 70] 201 rigid atoms, others: [32, 33, 2, 3, 4, 37, 38, 10, 11, 12, 13, 14, 34, 35, 36, 29, 30, 31] set([0, 1, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41, 42, 43]) total number of confs: 438 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581159 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581159 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581159/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581159 Building REAL300025581160 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581160' /scratch/stefan/7787361/working/building/REAL300025581160 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581160 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581160/0 /scratch/stefan/7787361/working/building/REAL300025581160 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/666 `/scratch/stefan/7787361/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581160 none CC(C)(C)OC(=O)N[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 180, 150, 180, 122, 122, 122, 122, 52, 119, 52, 52, 21, 9, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 150, 122, 122, 52, 21, 21, 9, 9] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 638 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581160 none CC(C)(C)OC(=O)N[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 25, 26, 26, 14, 8, 14, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 41, 49, 122, 122, 122, 122, 122, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 1, 1, 11, 41, 41, 49, 49] 201 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581160 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581160 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581160/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581160 Building REAL300025581161 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581161' /scratch/stefan/7787361/working/building/REAL300025581161 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581161 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581161/0 /scratch/stefan/7787361/working/building/REAL300025581161 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/667 `/scratch/stefan/7787361/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N2C)=C1) `REAL300025581161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581161 none CC1=CC=CC(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 95, 95, 95, 95, 39, 39, 39, 17, 7, 1, 1, 1, 1, 1, 1, 1, 95, 95, 201, 201, 201, 201, 201, 201, 201, 95, 95, 39, 17, 17, 7, 7, 95, 95, 95, 201] 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: 405 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581161 none CC1=CC=CC(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 35, 39, 95, 95, 95, 95, 95, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 8, 35, 35, 39, 39, 2, 2, 2, 7] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581161 none CC1=CC=CC(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)N2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 37, 37, 37, 109, 117, 201, 201, 201, 201, 201, 7, 7, 1, 2, 2, 2, 1, 1, 1, 7, 7, 37, 109, 109, 117, 117, 7, 7, 7, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 23, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581161 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581161 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581161/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581161 Building REAL300025581162 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581162' /scratch/stefan/7787361/working/building/REAL300025581162 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581162 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581162/0 /scratch/stefan/7787361/working/building/REAL300025581162 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/668 `/scratch/stefan/7787361/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCO[C@H]1C1=CC=NC=C1) `REAL300025581162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581162 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCO[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 5, 29, 29, 111, 133, 201, 201, 201, 201, 201, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 29, 111, 111, 133, 133, 5, 5, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 640 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581162 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCO[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 61, 87, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 11, 61, 61, 87, 87, 1, 1, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 537 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581162 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCO[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 25, 9, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 74, 25, 25, 9, 9, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 594 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581162 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581162 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581162/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581162 Building REAL300025581163 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581163' /scratch/stefan/7787361/working/building/REAL300025581163 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581163 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581163/0 /scratch/stefan/7787361/working/building/REAL300025581163 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/669 `/scratch/stefan/7787361/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=CNC2=O)=C1) `REAL300025581163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581163 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=CNC2=O)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 20, 20, 89, 98, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 20, 89, 89, 98, 98, 6, 6, 6, 1, 1, 1, 6] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 21, 31] 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, 34]) total number of confs: 531 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581163 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=CNC2=O)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 39, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 5, 29, 29, 39, 39, 1, 1, 1, 6, 6, 6, 1] 201 rigid atoms, others: [1, 34, 11, 12, 13, 14, 15, 16, 22, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581163 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=CNC2=O)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 56, 130, 130, 130, 130, 130, 201, 201, 201, 201, 201, 130, 56, 19, 19, 8, 8, 130, 130, 130, 201, 201, 201, 130] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581163 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581163 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581163/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581163 Building REAL300025581164 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581164' /scratch/stefan/7787361/working/building/REAL300025581164 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581164 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581164/0 /scratch/stefan/7787361/working/building/REAL300025581164 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/670 `/scratch/stefan/7787361/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(N2C=CNC2=O)C=C1) `REAL300025581164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581164 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(N2C=CNC2=O)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 1, 18, 18, 71, 118, 201, 201, 201, 201, 201, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 18, 71, 71, 118, 118, 9, 9, 1, 1, 1, 9, 9] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 649 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581164 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(N2C=CNC2=O)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 20, 36, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 4, 20, 20, 36, 36, 1, 1, 9, 9, 9, 1, 1] 201 rigid atoms, others: [1, 34, 33, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581164 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(N2C=CNC2=O)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 70, 91, 91, 75, 76, 201, 201, 201, 201, 201, 91, 91, 69, 24, 24, 8, 8, 91, 91, 201, 201, 201, 91, 91] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 506 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581164 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581164 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581164/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581164 Building REAL300025581165 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581165' /scratch/stefan/7787361/working/building/REAL300025581165 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581165 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581165/0 /scratch/stefan/7787361/working/building/REAL300025581165 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/671 `/scratch/stefan/7787361/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC(F)(F)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581165 none CC(C)(C)OC(=O)NCC(F)(F)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 164, 201, 114, 84, 79, 92, 92, 29, 29, 29, 11, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 114, 114, 79, 79, 29, 11, 11, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 850 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581165 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581165 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581165/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581165 Building REAL300025581166 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581166' /scratch/stefan/7787361/working/building/REAL300025581166 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581166 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581166/0 /scratch/stefan/7787361/working/building/REAL300025581166 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/672 `/scratch/stefan/7787361/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C2OC(F)(F)OC2=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581166 none O=C(CC1=CC=C2OC(F)(F)OC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 15, 7, 1, 1, 1, 1, 1, 1, 1, 101, 101, 201, 201, 201, 42, 15, 15, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 574 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581166 none O=C(CC1=CC=C2OC(F)(F)OC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 78, 85, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 17, 78, 78, 85, 85] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 516 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581166 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581166 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581166/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581166 Building REAL300025581167 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581167' /scratch/stefan/7787361/working/building/REAL300025581167 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581167 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581167/0 /scratch/stefan/7787361/working/building/REAL300025581167 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/673 `/scratch/stefan/7787361/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581167 none CC(C)(C)OC(=O)[C@@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 108, 201, 108, 108, 108, 108, 40, 108, 40, 40, 17, 8, 1, 1, 1, 1, 1, 1, 1, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 108, 108, 108, 40, 17, 17, 8, 8, 108, 108] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 614 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581167 none CC(C)(C)OC(=O)[C@@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 41, 42, 108, 108, 108, 108, 108, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 8, 41, 41, 42, 42, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 44, 43, 24, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581167 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581167 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581167/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581167 Building REAL300025581168 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581168' /scratch/stefan/7787361/working/building/REAL300025581168 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581168 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581168/0 /scratch/stefan/7787361/working/building/REAL300025581168 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/674 `/scratch/stefan/7787361/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1CN1C=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21) `REAL300025581168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581168 none COC1=CC=CC=C1CN1C=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 165, 201, 201, 104, 40, 40, 40, 40, 40, 40, 23, 23, 23, 15, 8, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 201, 201, 201, 201, 201, 201, 201, 104, 104, 40, 40, 23, 15, 15, 8, 8, 40, 40] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 739 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581168 none COC1=CC=CC=C1CN1C=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 17, 17, 17, 13, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 40, 40, 40, 40, 40, 1, 1, 1, 27, 27, 27, 17, 17, 17, 17, 6, 6, 1, 1, 5, 15, 15, 15, 15, 1, 1] 201 rigid atoms, others: [45, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 46, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581168 none COC1=CC=CC=C1CN1C=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 37, 37, 37, 101, 101, 201, 201, 201, 201, 201, 17, 17, 17, 4, 4, 4, 1, 1, 1, 1, 5, 5, 17, 17, 37, 101, 101, 101, 101, 17, 17] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 607 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581168 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581168 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581168/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581168 Building REAL300025581169 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581169' /scratch/stefan/7787361/working/building/REAL300025581169 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581169 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581169/0 /scratch/stefan/7787361/working/building/REAL300025581169 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/675 `/scratch/stefan/7787361/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC12CCCCC1C2(F)F)NCCC1=NC(=O)O[N-]1) `REAL300025581169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581169 none O=C(CC12CCCCC1C2(F)F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 169, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 19, 19, 8, 8] 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]) total number of confs: 720 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581169 none O=C(CC12CCCCC1C2(F)F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 99, 105, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 99, 99, 105, 105] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 35, 36, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 541 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581169 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581169 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581169/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581169 Building REAL300025581170 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581170' /scratch/stefan/7787361/working/building/REAL300025581170 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581170 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581170/0 /scratch/stefan/7787361/working/building/REAL300025581170 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/676 `/scratch/stefan/7787361/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C) `REAL300025581170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581170 none CC1=CC(Br)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [158, 158, 144, 158, 158, 158, 100, 101, 101, 22, 8, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 158, 148, 158, 100, 22, 22, 8, 8, 158, 158, 158] 158 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]) total number of confs: 433 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581170 none CC1=CC(Br)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 51, 74, 158, 158, 158, 158, 158, 1, 1, 2, 2, 2, 1, 1, 9, 51, 51, 74, 74, 2, 2, 2] 158 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 23, 24] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 443 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581170 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581170 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581170/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581170 Building REAL300025581171 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581171' /scratch/stefan/7787361/working/building/REAL300025581171 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581171 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581171/0 /scratch/stefan/7787361/working/building/REAL300025581171 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/677 `/scratch/stefan/7787361/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C([C@@H]2C[C@H]2CC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581171 none COC1=CC=C([C@@H]2C[C@H]2CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 198, 201, 201, 198, 198, 198, 198, 131, 198, 40, 41, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 198, 198, 131, 131, 40, 9, 9, 8, 8, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 723 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581171 none COC1=CC=C([C@@H]2C[C@H]2CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 40, 40, 40, 115, 115, 198, 198, 198, 198, 198, 4, 4, 4, 4, 4, 4, 4, 1, 1, 7, 7, 40, 115, 115, 115, 115, 4, 4] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 569 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581171 none COC1=CC=C([C@@H]2C[C@H]2CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 13, 68, 68, 68, 136, 136, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 4, 4, 13, 13, 68, 136, 136, 136, 136, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 23, 24, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 631 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581171 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581171 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581171/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581171 Building REAL300025581172 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581172' /scratch/stefan/7787361/working/building/REAL300025581172 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581172 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581172/0 /scratch/stefan/7787361/working/building/REAL300025581172 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/678 `/scratch/stefan/7787361/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(OCC2=CC=CC=C2)C=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581172 none O=C(CC1=CC=C(OCC2=CC=CC=C2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 127, 135, 135, 127, 135, 201, 201, 201, 201, 201, 201, 201, 135, 135, 15, 7, 1, 1, 1, 1, 1, 1, 1, 127, 127, 135, 135, 201, 201, 201, 201, 201, 201, 201, 135, 135, 39, 15, 15, 7, 7] 201 rigid atoms, others: [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: 697 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581172 none O=C(CC1=CC=C(OCC2=CC=CC=C2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 93, 99, 201, 201, 201, 201, 201, 9, 9, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6, 6, 28, 93, 93, 99, 99] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 564 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581172 none O=C(CC1=CC=C(OCC2=CC=CC=C2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 1, 8, 8, 32, 36, 135, 135, 135, 135, 135, 4, 4, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 1, 8, 32, 32, 36, 36] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 38, 28, 29, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581172 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581172 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581172/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581172 Building REAL300025581173 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581173' /scratch/stefan/7787361/working/building/REAL300025581173 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581173 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581173/0 /scratch/stefan/7787361/working/building/REAL300025581173 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/679 `/scratch/stefan/7787361/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2C(Cl)=CC=CN2N=C1) `REAL300025581173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581173 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C(Cl)=CC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 56, 80, 156, 156, 156, 156, 156, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 56, 56, 80, 80, 1, 1, 1, 1] 156 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 442 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581173 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C(Cl)=CC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [83, 82, 24, 8, 1, 1, 1, 1, 1, 1, 1, 82, 156, 156, 156, 156, 156, 156, 156, 156, 156, 82, 24, 24, 8, 8, 156, 156, 156, 156] 156 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581173 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581173 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581173/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581173 Building REAL300025581174 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581174' /scratch/stefan/7787361/working/building/REAL300025581174 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581174 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581174/0 /scratch/stefan/7787361/working/building/REAL300025581174 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/680 `/scratch/stefan/7787361/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC(Br)=C1F) `REAL300025581174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581174 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC(Br)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 96, 96, 96, 24, 8, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 153, 153, 153, 153, 96, 24, 24, 8, 8, 153, 153] 153 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 389 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581174 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC(Br)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 51, 81, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 51, 51, 81, 81, 1, 1] 153 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581174 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581174 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581174/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581174 Building REAL300025581175 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581175' /scratch/stefan/7787361/working/building/REAL300025581175 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581175 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581175/0 /scratch/stefan/7787361/working/building/REAL300025581175 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/681 `/scratch/stefan/7787361/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=NC(Cl)=CC=C2S1) `REAL300025581175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581175 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=NC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 16, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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: [12, 1, 12, 12, 59, 84, 139, 139, 139, 140, 140, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 59, 59, 85, 85, 1, 1, 1] 140 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 444 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581175 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=NC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 16, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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: [79, 79, 24, 8, 1, 1, 1, 1, 1, 1, 1, 79, 140, 140, 140, 140, 140, 139, 139, 139, 139, 78, 25, 25, 8, 8, 140, 139, 140] 140 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581175 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581175 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581175/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581175 Building REAL300025581176 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581176' /scratch/stefan/7787361/working/building/REAL300025581176 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581176 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581176/0 /scratch/stefan/7787361/working/building/REAL300025581176 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/682 `/scratch/stefan/7787361/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C2=CC=NC=C12) `REAL300025581176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581176 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C2=CC=NC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [10, 1, 10, 10, 51, 86, 186, 186, 186, 186, 186, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 51, 51, 86, 86, 1, 1, 1, 1, 1] 186 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 520 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581176 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C2=CC=NC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [104, 104, 23, 8, 1, 1, 1, 1, 1, 1, 1, 104, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 104, 23, 23, 8, 8, 186, 186, 186, 186, 186] 186 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581176 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581176 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581176/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581176 Building REAL300025581177 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581177' /scratch/stefan/7787361/working/building/REAL300025581177 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581177 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581177/0 /scratch/stefan/7787361/working/building/REAL300025581177 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/683 `/scratch/stefan/7787361/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)N=C2C=C(Cl)C=CN21) `REAL300025581177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581177 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)N=C2C=C(Cl)C=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 8, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 7, 7, 36, 64, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 36, 36, 64, 64, 1, 1, 1] 159 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581177 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)N=C2C=C(Cl)C=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 8, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [104, 104, 24, 8, 1, 1, 1, 1, 1, 1, 1, 104, 159, 159, 159, 159, 159, 159, 159, 159, 159, 159, 104, 24, 24, 8, 8, 159, 159, 159] 159 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581177 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581177 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581177/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581177 Building REAL300025581178 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581178' /scratch/stefan/7787361/working/building/REAL300025581178 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581178 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581178/0 /scratch/stefan/7787361/working/building/REAL300025581178 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/684 `/scratch/stefan/7787361/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CSC=C1Br)NCCC1=NC(=O)O[N-]1) `REAL300025581178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581178 none O=C(CCC1=CSC=C1Br)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Br', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 1, 17, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 130, 139, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 130, 130, 139, 139, 201, 201, 48, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 690 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581178 none O=C(CCC1=CSC=C1Br)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Br', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 1, 17, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 5, 1, 1, 1, 1, 1, 1, 1, 25, 25, 105, 107, 201, 201, 201, 201, 201, 7, 7, 5, 5, 1, 1, 25, 106, 106, 107, 107] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581178 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581178 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581178/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581178 Building REAL300025581179 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581179' /scratch/stefan/7787361/working/building/REAL300025581179 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581179 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581179/0 /scratch/stefan/7787361/working/building/REAL300025581179 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/685 `/scratch/stefan/7787361/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CC(N2CCCC2)=C1) `REAL300025581179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581179 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CC(N2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 1, 8, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 19, 91, 99, 201, 201, 201, 201, 201, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 19, 91, 91, 99, 99, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 30, 31] 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, 38]) total number of confs: 543 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: REAL300025581179 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CC(N2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 1, 8, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 34, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 5, 29, 29, 34, 34, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1] 201 rigid atoms, others: [1, 38, 11, 12, 13, 14, 15, 16, 17, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 246 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581179 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CC(N2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 1, 8, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 17, 8, 1, 1, 1, 1, 1, 1, 1, 52, 117, 117, 117, 117, 117, 117, 201, 201, 201, 201, 117, 52, 17, 17, 8, 8, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 117] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 412 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581179 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581179 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581179/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581179 Building REAL300025581180 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581180' /scratch/stefan/7787361/working/building/REAL300025581180 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581180 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581180/0 /scratch/stefan/7787361/working/building/REAL300025581180 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/686 `/scratch/stefan/7787361/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC(N1C=CC=N1)C(F)(F)F)NCCC1=NC(=O)O[N-]1) `REAL300025581180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581180 none O=C(CC(N1C=CC=N1)C(F)(F)F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 8, 5, 15, 15, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 2, 2, 2, 2, 2] 3 rigid atoms, others: [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]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581180 none O=C(CC(N1C=CC=N1)C(F)(F)F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 8, 5, 15, 15, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3] 3 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581180 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581180 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581180/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581180 Building REAL300025581181 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581181' /scratch/stefan/7787361/working/building/REAL300025581181 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581181 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581181/0 /scratch/stefan/7787361/working/building/REAL300025581181 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/687 `/scratch/stefan/7787361/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(S(=O)(=O)C(F)(F)F)=C1) `REAL300025581181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581181 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(S(=O)(=O)C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 43, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 7, 8, 1, 5, 29, 29, 43, 43, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581181 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(S(=O)(=O)C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 58, 142, 142, 142, 142, 142, 201, 201, 201, 201, 201, 201, 142, 58, 19, 19, 8, 8, 142, 142, 142, 142] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 667 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581181 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581181 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581181/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581181 Building REAL300025581182 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581182' /scratch/stefan/7787361/working/building/REAL300025581182 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581182 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581182/0 /scratch/stefan/7787361/working/building/REAL300025581182 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/688 `/scratch/stefan/7787361/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)N=C2C=CSC2=C1) `REAL300025581182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581182 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)N=C2C=CSC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 8, 1, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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: [7, 1, 7, 7, 43, 67, 136, 136, 136, 136, 136, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 43, 43, 67, 67, 1, 1, 1] 136 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581182 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)N=C2C=CSC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 8, 1, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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: [84, 84, 24, 8, 1, 1, 1, 1, 1, 1, 1, 84, 136, 136, 136, 136, 136, 136, 136, 136, 136, 84, 24, 24, 8, 8, 136, 136, 136] 136 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581182 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581182 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581182/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581182 Building REAL300025581183 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581183' /scratch/stefan/7787361/working/building/REAL300025581183 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581183 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581183/0 /scratch/stefan/7787361/working/building/REAL300025581183 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/689 `/scratch/stefan/7787361/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC(=O)N(C2=CC=CC(F)=C2)C1) `REAL300025581183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581183 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC(=O)N(C2=CC=CC(F)=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 30, 30, 106, 107, 201, 201, 201, 201, 201, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 30, 106, 106, 107, 107, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [35, 36, 37, 38, 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, 39, 40]) total number of confs: 567 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581183 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC(=O)N(C2=CC=CC(F)=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 33, 34, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 9, 33, 33, 34, 34, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 40, 11, 12, 13, 14, 15, 16, 17, 24, 39, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581183 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC(=O)N(C2=CC=CC(F)=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 11, 7, 1, 1, 1, 1, 1, 1, 1, 27, 69, 69, 69, 69, 69, 69, 201, 201, 201, 201, 201, 201, 69, 27, 11, 11, 7, 7, 69, 69, 69, 69, 69, 201, 201, 201, 201, 69, 69] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 393 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581183 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581183 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581183/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581183 Building REAL300025581184 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581184' /scratch/stefan/7787361/working/building/REAL300025581184 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581184 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581184/0 /scratch/stefan/7787361/working/building/REAL300025581184 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/690 `/scratch/stefan/7787361/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2CCCC(CC(=O)NCCC3=NC(=O)O[N-]3)C2=C1) `REAL300025581184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581184 none COC(=O)C1=CC=C2CCCC(CC(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 142, 201, 142, 142, 142, 142, 142, 142, 142, 122, 43, 43, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 142, 142, 201, 201, 201, 142, 142, 142, 142, 142, 142, 142, 142, 142, 122, 122, 42, 8, 9, 8, 8, 142] 201 rigid atoms, others: [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]) total number of confs: 746 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581184 none COC(=O)C1=CC=C2CCCC(CC(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 23, 23, 23, 72, 72, 142, 142, 142, 142, 142, 1, 1, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 72, 72, 72, 72, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 408 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581184 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581184 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581184/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581184 Building REAL300025581185 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581185' /scratch/stefan/7787361/working/building/REAL300025581185 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581185 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581185/0 /scratch/stefan/7787361/working/building/REAL300025581185 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/691 `/scratch/stefan/7787361/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC=CC1) `REAL300025581185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581185 none CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 65, 201, 33, 33, 33, 14, 7, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 201, 201, 201, 201, 201, 201, 201, 201, 201, 33, 14, 14, 7, 7, 65, 65, 65, 65, 65, 65] 201 rigid atoms, others: [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, 39, 40, 41, 42]) total number of confs: 573 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581185 none CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 1, 7, 1, 1, 4, 4, 4, 20, 26, 65, 65, 65, 65, 65, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 20, 20, 26, 26, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [5, 38, 7, 8, 41, 42, 39, 40, 19, 20, 21, 22, 37] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581185 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581185 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581185/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581185 Building REAL300025581186 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581186' /scratch/stefan/7787361/working/building/REAL300025581186 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581186 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581186/0 /scratch/stefan/7787361/working/building/REAL300025581186 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/692 `/scratch/stefan/7787361/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)C(C)(C)C) `REAL300025581186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581186 none CC(C)(C)OC(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 160, 118, 160, 71, 71, 71, 21, 8, 1, 1, 1, 1, 1, 1, 1, 116, 121, 121, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 71, 21, 21, 8, 8, 121, 121, 121, 121, 121, 121, 121, 121, 121] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 766 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581186 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581186 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581186/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581186 Building REAL300025581187 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581187' /scratch/stefan/7787361/working/building/REAL300025581187 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581187 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581187/0 /scratch/stefan/7787361/working/building/REAL300025581187 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/693 `/scratch/stefan/7787361/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)C1CC1) `REAL300025581187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581187 none CC(C)(C)OC(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 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, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 13, 2, 13, 1, 2, 12, 12, 12, 39, 39, 128, 128, 128, 128, 128, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 12, 39, 39, 39, 39, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 7, 40, 41, 39, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581187 none CC(C)(C)OC(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 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, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 198, 127, 198, 40, 40, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 123, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 39, 8, 8, 8, 8, 128, 128, 128, 128, 128] 201 rigid atoms, others: [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, 39, 40, 41]) total number of confs: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581187 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581187 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581187/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581187 Building REAL300025581188 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581188' /scratch/stefan/7787361/working/building/REAL300025581188 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581188 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581188/0 /scratch/stefan/7787361/working/building/REAL300025581188 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/694 `/scratch/stefan/7787361/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC2CCC1C2) `REAL300025581188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581188 none CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC2CCC1C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 176, 51, 176, 50, 51, 51, 20, 8, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 50, 20, 20, 8, 8, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 557 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581188 none CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC2CCC1C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 7, 1, 7, 1, 1, 2, 2, 2, 8, 14, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 8, 8, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 5, 7, 8, 41, 42, 39, 44, 45, 46, 47, 48, 40, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/7787361/working/building/REAL300025581188 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581188 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581188/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581188 Building REAL300025581189 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581189' /scratch/stefan/7787361/working/building/REAL300025581189 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581189 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581189/0 /scratch/stefan/7787361/working/building/REAL300025581189 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/695 `/scratch/stefan/7787361/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025581189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581189 none CC(C)(C)OC(=O)C1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 196, 63, 196, 63, 63, 63, 31, 31, 31, 15, 8, 1, 1, 1, 1, 1, 1, 1, 63, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 63, 63, 63, 63, 63, 63, 31, 15, 15, 8, 8, 63, 63, 63, 63] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 598 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581189 none CC(C)(C)OC(=O)C1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 11, 1, 11, 1, 1, 1, 1, 1, 4, 4, 4, 22, 24, 63, 63, 63, 63, 63, 1, 1, 17, 17, 17, 16, 16, 16, 17, 17, 17, 1, 1, 1, 1, 1, 1, 4, 22, 22, 24, 24, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 44, 45, 46, 47, 22, 23, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581189 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581189 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581189/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581189 Building REAL300025581190 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581190' /scratch/stefan/7787361/working/building/REAL300025581190 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581190 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581190/0 /scratch/stefan/7787361/working/building/REAL300025581190 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/696 `/scratch/stefan/7787361/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1=CC=CC=C1) `REAL300025581190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581190 none CN1C=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 31, 31, 31, 102, 123, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 31, 102, 102, 123, 123, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 611 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581190 none CN1C=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 79, 79, 79, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 78, 24, 24, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581190 none CN1C=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 13, 65, 92, 201, 201, 201, 201, 201, 1, 1, 4, 4, 1, 4, 4, 2, 2, 2, 1, 1, 13, 65, 64, 92, 92, 4, 4, 1, 4, 4] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 558 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581190 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581190 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581190/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581190 Building REAL300025581191 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581191' /scratch/stefan/7787361/working/building/REAL300025581191 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581191 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581191/0 /scratch/stefan/7787361/working/building/REAL300025581191 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/697 `/scratch/stefan/7787361/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NCC(F)(F)F)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581191 none CC(C)[C@H](NCC(F)(F)F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 10, 5, 5, 15, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 137, 165, 52, 137, 137, 154, 188, 188, 188, 188, 52, 52, 8, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 165, 154, 188, 188, 51, 9, 9, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 923 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581191 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581191 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581191/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581191 Building REAL300025581192 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581192' /scratch/stefan/7787361/working/building/REAL300025581192 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581192 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581192/0 /scratch/stefan/7787361/working/building/REAL300025581192 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/698 `/scratch/stefan/7787361/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1CCOCC1) `REAL300025581192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581192 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 20, 77, 95, 201, 201, 201, 201, 201, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 20, 77, 77, 95, 95, 3, 3, 3, 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, 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]) total number of confs: 530 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581192 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 182, 181, 73, 73, 73, 22, 8, 1, 1, 1, 1, 1, 1, 1, 182, 182, 182, 182, 201, 201, 201, 201, 201, 182, 182, 182, 181, 72, 22, 22, 8, 8, 182, 182, 182, 201, 201, 201, 201, 201, 201, 201, 201, 201] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 465 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581192 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 59, 79, 181, 181, 181, 181, 181, 1, 1, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 12, 59, 59, 79, 79, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 489 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581192 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581192 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581192/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581192 Building REAL300025581193 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581193' /scratch/stefan/7787361/working/building/REAL300025581193 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581193 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581193/0 /scratch/stefan/7787361/working/building/REAL300025581193 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/699 `/scratch/stefan/7787361/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(NCC(F)(F)F)=N1) `REAL300025581193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581193 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(NCC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 52, 52, 52, 17, 8, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 162, 201, 201, 201, 201, 124, 124, 124, 124, 124, 52, 17, 17, 8, 8, 124, 162, 201, 201] 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, 34, 35, 36]) total number of confs: 629 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581193 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(NCC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 29, 33, 124, 124, 124, 124, 124, 1, 1, 1, 5, 22, 22, 22, 22, 1, 2, 2, 2, 1, 5, 29, 29, 33, 33, 1, 5, 22, 22] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 15, 16, 17, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 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 /scratch/stefan/7787361/working/building/REAL300025581193 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581193 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581193/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581193 Building REAL300025581194 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581194' /scratch/stefan/7787361/working/building/REAL300025581194 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581194 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581194/0 /scratch/stefan/7787361/working/building/REAL300025581194 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/700 `/scratch/stefan/7787361/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC=C(F)C=C2)=NO1) `REAL300025581194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581194 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC=C(F)C=C2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 43, 43, 119, 126, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 42, 119, 119, 126, 126, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 592 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581194 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC=C(F)C=C2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 48, 68, 197, 197, 197, 198, 198, 1, 1, 1, 1, 7, 7, 1, 1, 7, 7, 1, 1, 10, 48, 48, 69, 69, 1, 7, 7, 7, 7] 201 rigid atoms, others: [1, 11, 12, 13, 14, 21, 22, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 476 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581194 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC=C(F)C=C2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 94, 198, 198, 198, 201, 201, 201, 201, 201, 201, 197, 197, 93, 24, 24, 8, 8, 198, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581194 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581194 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581194/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581194 Building REAL300025581195 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581195' /scratch/stefan/7787361/working/building/REAL300025581195 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581195 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581195/0 /scratch/stefan/7787361/working/building/REAL300025581195 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/701 `/scratch/stefan/7787361/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Br) `REAL300025581195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581195 none CC(C)(C)N1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 166, 166, 166, 85, 85, 85, 24, 8, 1, 1, 1, 1, 1, 1, 1, 166, 166, 166, 166, 166, 166, 166, 166, 166, 166, 166, 166, 85, 24, 24, 8, 8] 166 rigid atoms, others: [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]) total number of confs: 397 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581195 none CC(C)(C)N1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 45, 80, 166, 166, 166, 166, 166, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 7, 45, 45, 80, 80] 166 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 24, 25, 26, 30] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28, 29, 31]) total number of confs: 495 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581195 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581195 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581195/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581195 Building REAL300025581196 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581196' /scratch/stefan/7787361/working/building/REAL300025581196 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581196 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581196/0 /scratch/stefan/7787361/working/building/REAL300025581196 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/702 `/scratch/stefan/7787361/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2=C(C=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)C1) `REAL300025581196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581196 none CC(C)(C)OC(=O)N1CCC2=C(C=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 148, 107, 148, 107, 107, 106, 106, 107, 107, 51, 51, 51, 20, 8, 1, 1, 1, 1, 1, 1, 1, 106, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 107, 106, 106, 107, 50, 20, 20, 8, 8, 107, 107] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 516 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581196 none CC(C)(C)OC(=O)N1CCC2=C(C=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 8, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 33, 39, 106, 106, 106, 106, 106, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 33, 33, 39, 39, 1, 1] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 47, 40, 46, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581196 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581196 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581196/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581196 Building REAL300025581197 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581197' /scratch/stefan/7787361/working/building/REAL300025581197 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581197 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581197/0 /scratch/stefan/7787361/working/building/REAL300025581197 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/703 `/scratch/stefan/7787361/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)N(C)C(=O)OC(C)(C)C) `REAL300025581197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581197 none C[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)N(C)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 113, 43, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 113, 139, 139, 164, 164, 201, 201, 201, 201, 113, 110, 113, 42, 8, 8, 8, 8, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 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: 693 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581197 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581197 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581197/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581197 Building REAL300025581198 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581198' /scratch/stefan/7787361/working/building/REAL300025581198 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581198 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581198/0 /scratch/stefan/7787361/working/building/REAL300025581198 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/704 `/scratch/stefan/7787361/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2=C(C1)SC(C(=O)NCCC1=NC(=O)O[N-]1)=C2) `REAL300025581198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581198 none CC(C)(C)OC(=O)N1CC2=C(C1)SC(C(=O)NCCC1=NC(=O)O[N-]1)=C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 201, 145, 97, 145, 97, 97, 97, 97, 97, 97, 55, 55, 55, 20, 8, 1, 1, 1, 1, 1, 1, 1, 97, 201, 201, 201, 200, 201, 200, 201, 201, 201, 97, 97, 97, 97, 54, 20, 20, 8, 8, 97] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 547 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581198 none CC(C)(C)OC(=O)N1CC2=C(C1)SC(C(=O)NCCC1=NC(=O)O[N-]1)=C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 8, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 36, 39, 96, 96, 96, 96, 96, 1, 11, 11, 11, 11, 10, 11, 11, 11, 11, 1, 1, 1, 1, 8, 35, 35, 40, 40, 1] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 44, 25, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581198 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581198 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581198/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581198 Building REAL300025581199 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581199' /scratch/stefan/7787361/working/building/REAL300025581199 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581199 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581199/0 /scratch/stefan/7787361/working/building/REAL300025581199 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/705 `/scratch/stefan/7787361/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1OC(F)(F)O2) `REAL300025581199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581199 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1OC(F)(F)O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 69, 92, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 69, 69, 92, 92, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 534 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581199 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1OC(F)(F)O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 23, 23, 8, 8, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581199 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581199 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581199/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581199 Building REAL300025581200 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581200' /scratch/stefan/7787361/working/building/REAL300025581200 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581200 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581200/0 /scratch/stefan/7787361/working/building/REAL300025581200 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/706 `/scratch/stefan/7787361/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(C(F)(F)F)=C1) `REAL300025581200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581200 none CN(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 140, 201, 140, 140, 62, 62, 62, 20, 8, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 140, 140, 201, 201, 201, 201, 201, 201, 140, 61, 20, 21, 8, 8, 140, 140] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 570 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581200 none CN(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 5, 5, 5, 29, 49, 140, 140, 140, 140, 140, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 5, 29, 29, 49, 49, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 36, 30, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 345 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581200 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581200 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581200/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581200 Building REAL300025581201 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581201' /scratch/stefan/7787361/working/building/REAL300025581201 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581201 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581201/0 /scratch/stefan/7787361/working/building/REAL300025581201 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/707 `/scratch/stefan/7787361/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(SC(F)(F)F)=C1) `REAL300025581201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581201 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(SC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 15, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 1, 3, 13, 13, 15, 15, 1, 1, 1, 1] 66 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 21, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581201 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(SC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 17, 8, 1, 1, 1, 1, 1, 1, 1, 43, 56, 56, 56, 56, 56, 66, 66, 66, 66, 56, 43, 17, 17, 8, 8, 56, 56, 56, 56] 66 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581201 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581201 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581201/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581201 Building REAL300025581202 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581202' /scratch/stefan/7787361/working/building/REAL300025581202 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581202 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581202/0 /scratch/stefan/7787361/working/building/REAL300025581202 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/708 `/scratch/stefan/7787361/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CC(=O)NCCC1=NC(=O)O[N-]1)C(=O)OC(C)(C)C) `REAL300025581202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581202 none CC(C)N(CC(=O)NCCC1=NC(=O)O[N-]1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 134, 40, 40, 40, 15, 7, 1, 1, 1, 1, 1, 1, 1, 172, 201, 201, 201, 201, 201, 201, 172, 172, 172, 172, 172, 172, 172, 134, 134, 40, 15, 15, 7, 7, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581202 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581202 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581202/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581202 Building REAL300025581203 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581203' /scratch/stefan/7787361/working/building/REAL300025581203 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581203 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581203/0 /scratch/stefan/7787361/working/building/REAL300025581203 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/709 `/scratch/stefan/7787361/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N=NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581203 none NC(=O)N=NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 145, 201, 145, 127, 127, 127, 127, 54, 54, 54, 19, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 201, 201, 127, 127, 54, 19, 19, 8, 8, 127, 127] 201 rigid atoms, others: [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: 553 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581203 none NC(=O)N=NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 30, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 38, 127, 127, 127, 127, 127, 1, 1, 31, 31, 1, 1, 5, 29, 29, 38, 38, 1, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581203 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581203 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581203/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581203 Building REAL300025581204 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581204' /scratch/stefan/7787361/working/building/REAL300025581204 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581204 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581204/0 /scratch/stefan/7787361/working/building/REAL300025581204 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/710 `/scratch/stefan/7787361/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2C=C(C(=O)NCCC3=NC(=O)O[N-]3)NC2=CC=C1Br) `REAL300025581204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581204 none CC1=C2C=C(C(=O)NCCC3=NC(=O)O[N-]3)NC2=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 68, 68, 68, 24, 8, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 68, 25, 25, 8, 8, 116, 116, 116] 116 rigid atoms, others: [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]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581204 none CC1=C2C=C(C(=O)NCCC3=NC(=O)O[N-]3)NC2=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 54, 72, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 54, 54, 72, 72, 1, 1, 1] 116 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 16, 17, 18, 19, 20, 21, 25, 33, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 373 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581204 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581204 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581204/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581204 Building REAL300025581205 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581205' /scratch/stefan/7787361/working/building/REAL300025581205 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581205 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581205/0 /scratch/stefan/7787361/working/building/REAL300025581205 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/711 `/scratch/stefan/7787361/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581205 none COC1=CC=CC=C1C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 175, 50, 175, 175, 50, 50, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 49, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 723 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581205 none COC1=CC=CC=C1C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 75, 89, 201, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 1, 24, 75, 75, 89, 89] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 536 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581205 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581205 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581205/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581205 Building REAL300025581206 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581206' /scratch/stefan/7787361/working/building/REAL300025581206 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581206 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581206/0 /scratch/stefan/7787361/working/building/REAL300025581206 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/712 `/scratch/stefan/7787361/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCC2=NC(=O)O[N-]2)CC(C2=CC=CC=C2)=NO1) `REAL300025581206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581206 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CC(C2=CC=CC=C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 38, 38, 38, 109, 125, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 38, 109, 109, 125, 125, 7, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 606 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581206 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CC(C2=CC=CC=C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 88, 88, 88, 24, 8, 1, 1, 1, 1, 1, 1, 1, 199, 199, 199, 201, 201, 201, 201, 201, 199, 199, 199, 199, 199, 88, 24, 24, 8, 8, 199, 199, 201, 201, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 599 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581206 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CC(C2=CC=CC=C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 11, 11, 11, 57, 77, 199, 199, 199, 199, 199, 1, 1, 1, 7, 7, 2, 7, 7, 1, 1, 2, 2, 2, 11, 57, 57, 77, 77, 1, 1, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 32, 13, 14, 15, 21, 22, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 506 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581206 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581206 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581206/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581206 Building REAL300025581207 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581207' /scratch/stefan/7787361/working/building/REAL300025581207 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581207 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581207/0 /scratch/stefan/7787361/working/building/REAL300025581207 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/713 `/scratch/stefan/7787361/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2=CC=CN=C2)=N1) `REAL300025581207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581207 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 34, 34, 99, 114, 201, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 34, 99, 99, 115, 115, 4, 1, 1, 1, 1] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 576 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581207 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 50, 62, 140, 140, 140, 140, 140, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 12, 49, 49, 62, 62, 1, 4, 4, 4, 4] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 21, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 361 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581207 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 86, 140, 140, 140, 140, 201, 201, 201, 201, 201, 137, 86, 24, 24, 8, 8, 140, 201, 201, 201, 199] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581207 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581207 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581207/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581207 Building REAL300025581208 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581208' /scratch/stefan/7787361/working/building/REAL300025581208 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581208 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581208/0 /scratch/stefan/7787361/working/building/REAL300025581208 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/714 `/scratch/stefan/7787361/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(NC(=O)C(F)(F)F)C=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581208 none O=C(CC1=CC=C(NC(=O)C(F)(F)F)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 15, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 79, 95, 95, 87, 95, 201, 201, 201, 201, 201, 201, 95, 95, 13, 7, 1, 1, 1, 1, 1, 1, 1, 79, 79, 95, 95, 201, 95, 95, 35, 13, 13, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 713 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581208 none O=C(CC1=CC=C(NC(=O)C(F)(F)F)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 15, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 9, 9, 35, 37, 95, 95, 95, 95, 95, 4, 4, 1, 1, 5, 1, 1, 9, 35, 35, 37, 37] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 14, 15, 27, 28, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 32, 33, 34, 35, 36]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581208 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581208 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581208/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581208 Building REAL300025581209 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581209' /scratch/stefan/7787361/working/building/REAL300025581209 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581209 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581209/0 /scratch/stefan/7787361/working/building/REAL300025581209 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/715 `/scratch/stefan/7787361/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)COC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025581209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581209 none CC(C)(C)OC(=O)COC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 194, 54, 194, 50, 33, 33, 33, 33, 33, 13, 13, 13, 5, 3, 1, 1, 1, 1, 1, 1, 1, 33, 201, 201, 201, 201, 201, 201, 201, 201, 201, 54, 54, 33, 33, 33, 13, 5, 5, 3, 3, 33] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 510 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581209 none CC(C)(C)OC(=O)COC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 36, 8, 36, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 17, 33, 33, 33, 33, 33, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8, 1, 1, 1, 5, 15, 15, 17, 17, 1] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581209 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581209 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581209/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581209 Building REAL300025581210 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581210' /scratch/stefan/7787361/working/building/REAL300025581210 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581210 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581210/0 /scratch/stefan/7787361/working/building/REAL300025581210 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/716 `/scratch/stefan/7787361/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC1=O) `REAL300025581210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581210 none COCCCN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 144, 113, 79, 79, 79, 45, 45, 45, 17, 8, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 201, 201, 201, 201, 201, 144, 144, 113, 113, 45, 17, 17, 8, 8, 79, 79] 201 rigid atoms, others: [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: 885 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581210 none COCCCN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 12, 6, 4, 1, 1, 1, 1, 1, 8, 8, 8, 30, 33, 79, 79, 79, 79, 79, 1, 1, 1, 1, 24, 24, 24, 12, 12, 6, 6, 4, 4, 8, 30, 30, 33, 33, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 19, 20, 21, 22, 38, 37] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581210 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581210 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581210/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581210 Building REAL300025581211 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581211' /scratch/stefan/7787361/working/building/REAL300025581211 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581211 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581211/0 /scratch/stefan/7787361/working/building/REAL300025581211 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/717 `/scratch/stefan/7787361/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1C=C(Br)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL300025581211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581211 none CC(C)(C)N1C=C(Br)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 121, 201, 201, 121, 121, 121, 121, 69, 69, 69, 20, 8, 1, 1, 1, 1, 1, 1, 1, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201, 121, 68, 21, 21, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 796 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581211 none CC(C)(C)N1C=C(Br)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 17, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 31, 44, 121, 121, 121, 121, 121, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 7, 31, 31, 44, 44] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 20, 30] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581211 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581211 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581211/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581211 Building REAL300025581212 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581212' /scratch/stefan/7787361/working/building/REAL300025581212 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581212 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581212/0 /scratch/stefan/7787361/working/building/REAL300025581212 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/718 `/scratch/stefan/7787361/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCCC[C@@H]1N1CCCC1=O) `REAL300025581212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581212 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCCC[C@@H]1N1CCCC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 5, 5, 5, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 4, 17, 29, 71, 71, 71, 71, 71, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 17, 17, 29, 29, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1] 71 rigid atoms, others: [38, 39, 40, 41, 42, 43, 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]) total number of confs: 194 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581212 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCCC[C@@H]1N1CCCC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 5, 5, 5, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 17, 29, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 17, 17, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 71 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43]) total number of confs: 194 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581212 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCCC[C@@H]1N1CCCC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 5, 5, 5, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 22, 8, 1, 1, 1, 1, 1, 1, 1, 48, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 48, 22, 22, 8, 8, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71] 71 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 251 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581212 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581212 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581212/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581212 Building REAL300025581213 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581213' /scratch/stefan/7787361/working/building/REAL300025581213 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581213 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581213/0 /scratch/stefan/7787361/working/building/REAL300025581213 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/719 `/scratch/stefan/7787361/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCO[C@H]1C1=CN=CC(Br)=C1) `REAL300025581213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581213 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCO[C@H]1C1=CN=CC(Br)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 8, 1, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 38, 38, 126, 130, 201, 201, 201, 201, 201, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 38, 126, 126, 130, 130, 7, 7, 7, 7, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 608 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581213 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCO[C@H]1C1=CN=CC(Br)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 8, 1, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 43, 46, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 9, 43, 43, 46, 46, 1, 1, 1, 1, 7, 7, 7] 201 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 291 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581213 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCO[C@H]1C1=CN=CC(Br)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 8, 1, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 1, 1, 1, 1, 1, 1, 1, 50, 131, 131, 131, 131, 131, 131, 131, 201, 201, 201, 201, 201, 201, 50, 16, 16, 8, 8, 131, 131, 131, 131, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 545 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581213 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581213 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581213/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581213 Building REAL300025581214 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581214' /scratch/stefan/7787361/working/building/REAL300025581214 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581214 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581214/0 /scratch/stefan/7787361/working/building/REAL300025581214 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/720 `/scratch/stefan/7787361/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](CNC(=O)OC(C)(C)C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581214 none CC(C)C[C@H](CNC(=O)OC(C)(C)C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 64, 45, 64, 63, 72, 158, 200, 200, 201, 201, 201, 201, 20, 20, 20, 8, 5, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 72, 72, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 45, 45, 20, 8, 8, 5, 5] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 771 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581214 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581214 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581214/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581214 Building REAL300025581215 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581215' /scratch/stefan/7787361/working/building/REAL300025581215 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581215 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581215/0 /scratch/stefan/7787361/working/building/REAL300025581215 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/721 `/scratch/stefan/7787361/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)C(C)(C)C2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21) `REAL300025581215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581215 none CN1C(=O)C(C)(C)C2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 132, 132, 132, 132, 132, 132, 55, 55, 55, 22, 8, 1, 1, 1, 1, 1, 1, 1, 132, 132, 131, 132, 132, 132, 132, 132, 132, 132, 132, 132, 132, 54, 22, 22, 8, 8, 132, 132] 132 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: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581215 none CN1C(=O)C(C)(C)C2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 43, 65, 132, 132, 132, 132, 132, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 43, 43, 65, 65, 1, 1] 132 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 40, 21, 22, 23, 33] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581215 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581215 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581215/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581215 Building REAL300025581216 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581216' /scratch/stefan/7787361/working/building/REAL300025581216 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581216 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581216/0 /scratch/stefan/7787361/working/building/REAL300025581216 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/722 `/scratch/stefan/7787361/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581216 none CC(C)(C)OC(=O)COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 197, 84, 197, 70, 19, 19, 35, 35, 19, 19, 19, 9, 7, 1, 1, 1, 1, 1, 1, 1, 35, 35, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 84, 35, 35, 19, 9, 9, 7, 7, 35, 35] 201 rigid atoms, others: [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]) total number of confs: 587 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581216 none CC(C)(C)OC(=O)COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 41, 40, 38, 5, 38, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 35, 35, 35, 35, 35, 1, 1, 41, 41, 41, 41, 40, 41, 41, 41, 41, 5, 5, 1, 1, 5, 15, 15, 15, 15, 1, 1] 201 rigid atoms, others: [45, 37, 38, 8, 9, 10, 11, 12, 13, 44, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581216 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581216 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581216/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581216 Building REAL300025581217 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581217' /scratch/stefan/7787361/working/building/REAL300025581217 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581217 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581217/0 /scratch/stefan/7787361/working/building/REAL300025581217 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/723 `/scratch/stefan/7787361/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(CCCC2)C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581217 none CC(C)(C)OC(=O)N1CC2(CCCC2)C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [192, 192, 192, 192, 150, 102, 150, 102, 102, 102, 102, 102, 102, 102, 76, 77, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 192, 192, 192, 192, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 76, 24, 24, 8, 8] 192 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 616 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581217 none CC(C)(C)OC(=O)N1CC2(CCCC2)C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 11, 12, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 35, 102, 102, 102, 102, 102, 13, 13, 13, 12, 12, 12, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 35, 35] 192 rigid atoms, others: [45, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 44, 40, 43, 41, 39, 15, 42, 37] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47, 48, 49, 50]) total number of confs: 270 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581217 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581217 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581217/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581217 Building REAL300025581218 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581218' /scratch/stefan/7787361/working/building/REAL300025581218 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581218 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581218/0 /scratch/stefan/7787361/working/building/REAL300025581218 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/724 `/scratch/stefan/7787361/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1C(F)(F)F) `REAL300025581218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581218 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 94, 94, 94, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 23, 23, 8, 8, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 451 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581218 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 7, 31, 59, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 1, 7, 31, 31, 59, 59, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 16, 17, 18, 19, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 463 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581218 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581218 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581218/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581218 Building REAL300025581219 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581219' /scratch/stefan/7787361/working/building/REAL300025581219 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581219 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581219/0 /scratch/stefan/7787361/working/building/REAL300025581219 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/725 `/scratch/stefan/7787361/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC1=CC=C(C(F)(F)F)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581219 none CNC1=CC=C(C(F)(F)F)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 198, 172, 201, 201, 201, 201, 201, 201, 74, 74, 74, 21, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 74, 21, 21, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 539 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581219 none CNC1=CC=C(C(F)(F)F)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 60, 84, 201, 201, 201, 201, 201, 8, 8, 8, 8, 1, 1, 1, 12, 60, 60, 84, 84] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 32, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 532 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581219 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581219 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581219/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581219 Building REAL300025581220 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581220' /scratch/stefan/7787361/working/building/REAL300025581220 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581220 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581220/0 /scratch/stefan/7787361/working/building/REAL300025581220 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/726 `/scratch/stefan/7787361/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC=CC(Br)=C2)=NO1) `REAL300025581220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581220 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC=CC(Br)=C2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 44, 44, 125, 148, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 44, 126, 126, 148, 148, 13, 1, 1, 1, 1] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 652 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581220 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC=CC(Br)=C2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 34, 41, 121, 121, 121, 121, 121, 1, 1, 1, 1, 13, 13, 9, 13, 13, 13, 1, 1, 6, 33, 33, 41, 41, 1, 13, 13, 12, 13] 201 rigid atoms, others: [1, 11, 12, 13, 14, 21, 22, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581220 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC=CC(Br)=C2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 64, 121, 121, 121, 201, 201, 201, 201, 201, 201, 121, 121, 63, 23, 23, 8, 8, 121, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 441 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581220 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581220 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581220/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581220 Building REAL300025581221 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581221' /scratch/stefan/7787361/working/building/REAL300025581221 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581221 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581221/0 /scratch/stefan/7787361/working/building/REAL300025581221 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/727 `/scratch/stefan/7787361/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC=C(Br)C=C2)=NO1) `REAL300025581221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581221 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC=C(Br)C=C2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 43, 43, 118, 124, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 42, 118, 118, 124, 124, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 586 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581221 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC=C(Br)C=C2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 49, 69, 197, 197, 197, 198, 198, 1, 1, 1, 1, 7, 7, 1, 6, 7, 7, 1, 1, 10, 48, 48, 69, 69, 1, 7, 7, 7, 7] 201 rigid atoms, others: [1, 11, 12, 13, 14, 21, 22, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581221 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2=CC=C(Br)C=C2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 94, 198, 198, 198, 201, 201, 201, 201, 201, 201, 197, 197, 93, 24, 24, 8, 8, 198, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 441 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581221 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581221 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581221/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581221 Building REAL300025581222 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581222' /scratch/stefan/7787361/working/building/REAL300025581222 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581222 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581222/0 /scratch/stefan/7787361/working/building/REAL300025581222 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/728 `/scratch/stefan/7787361/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(Cl)=CC=C2S1) `REAL300025581222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581222 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 12, 59, 87, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 58, 58, 87, 87, 1, 1, 1, 1] 147 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 461 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581222 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 80, 146, 146, 146, 146, 146, 146, 146, 146, 146, 80, 24, 24, 8, 8, 146, 146, 146, 146] 147 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581222 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581222 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581222/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581222 Building REAL300025581223 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581223' /scratch/stefan/7787361/working/building/REAL300025581223 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581223 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581223/0 /scratch/stefan/7787361/working/building/REAL300025581223 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/729 `/scratch/stefan/7787361/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581223 none COC1=CC=C([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 195, 201, 201, 195, 195, 195, 195, 56, 193, 56, 56, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 195, 195, 56, 19, 19, 8, 8, 201, 201] 201 rigid atoms, others: [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: 600 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581223 none COC1=CC=C([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 66, 72, 195, 195, 195, 195, 195, 7, 7, 7, 7, 7, 7, 7, 1, 1, 13, 66, 66, 72, 72, 7, 7] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 442 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581223 none COC1=CC=C([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 28, 28, 28, 107, 112, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 7, 7, 28, 107, 107, 112, 112, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22, 23, 36, 27, 28, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 543 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581223 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581223 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581223/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581223 Building REAL300025581224 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581224' /scratch/stefan/7787361/working/building/REAL300025581224 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581224 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581224/0 /scratch/stefan/7787361/working/building/REAL300025581224 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/730 `/scratch/stefan/7787361/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(=O)C2=CC=CO2)=C1) `REAL300025581224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581224 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(=O)C2=CC=CO2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 47, 47, 128, 128, 201, 201, 201, 201, 201, 21, 21, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 21, 47, 128, 128, 128, 128, 21, 21, 21, 1, 1, 1, 21] 201 rigid atoms, others: [32, 33, 34, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 603 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581224 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(=O)C2=CC=CO2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 24, 28, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 12, 12, 21, 21, 21, 21, 1, 5, 24, 24, 28, 28, 1, 1, 1, 21, 21, 21, 1] 201 rigid atoms, others: [1, 35, 11, 12, 13, 14, 15, 16, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581224 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(=O)C2=CC=CO2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 1, 1, 1, 1, 1, 1, 1, 39, 101, 101, 101, 101, 101, 193, 193, 201, 201, 201, 201, 101, 39, 15, 15, 7, 7, 101, 101, 101, 201, 201, 201, 101] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 528 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581224 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581224 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581224/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581224 Building REAL300025581225 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581225' /scratch/stefan/7787361/working/building/REAL300025581225 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581225 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581225/0 /scratch/stefan/7787361/working/building/REAL300025581225 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/731 `/scratch/stefan/7787361/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(C2CCCCC2)C=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581225 none O=C(CC1=CC=C(C2CCCCC2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 79, 110, 110, 79, 97, 201, 201, 201, 201, 201, 110, 110, 13, 7, 1, 1, 1, 1, 1, 1, 1, 79, 79, 110, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 110, 33, 13, 13, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 880 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581225 none O=C(CC1=CC=C(C2CCCCC2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 17, 17, 81, 89, 201, 201, 201, 201, 201, 7, 7, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 17, 81, 81, 89, 89] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 534 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581225 none O=C(CC1=CC=C(C2CCCCC2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 9, 9, 44, 48, 110, 110, 110, 110, 110, 4, 4, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 9, 44, 44, 48, 48] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 39, 13, 14, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581225 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581225 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581225/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581225 Building REAL300025581226 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581226' /scratch/stefan/7787361/working/building/REAL300025581226 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581226 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581226/0 /scratch/stefan/7787361/working/building/REAL300025581226 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/732 `/scratch/stefan/7787361/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025581226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581226 none CN(C)C(=O)C1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 136, 201, 136, 136, 136, 50, 50, 50, 17, 8, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 201, 201, 201, 201, 136, 136, 136, 136, 136, 136, 50, 17, 17, 8, 8, 136, 136, 136, 136] 201 rigid atoms, others: [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, 40, 41, 42]) total number of confs: 658 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581226 none CN(C)C(=O)C1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 6, 1, 4, 1, 1, 1, 1, 1, 12, 12, 12, 49, 52, 136, 136, 136, 136, 136, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 12, 49, 49, 52, 52, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 39, 40, 20, 21, 41, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38]) total number of confs: 314 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581226 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581226 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581226/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581226 Building REAL300025581227 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581227' /scratch/stefan/7787361/working/building/REAL300025581227 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581227 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581227/0 /scratch/stefan/7787361/working/building/REAL300025581227 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/733 `/scratch/stefan/7787361/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C=NC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581227 none CC1=C(Br)C=NC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 91, 91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 91, 25, 25, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 441 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581227 none CC1=C(Br)C=NC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 60, 88, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 10, 60, 60, 88, 88] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 557 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581227 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581227 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581227/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581227 Building REAL300025581228 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581228' /scratch/stefan/7787361/working/building/REAL300025581228 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581228 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581228/0 /scratch/stefan/7787361/working/building/REAL300025581228 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/734 `/scratch/stefan/7787361/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)N1CC2=CC=CC=C2C1=O) `REAL300025581228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581228 none CC(C)[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)N1CC2=CC=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 1, 5, 6, 18, 18, 18, 51, 51, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 18, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1] 85 rigid atoms, others: [3, 38, 39, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 279 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581228 none CC(C)[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)N1CC2=CC=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [82, 74, 82, 43, 74, 43, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 74, 84, 84, 84, 84, 84, 84, 84, 84, 84, 82, 82, 82, 82, 82, 82, 82, 43, 8, 8, 8, 8, 84, 84, 84, 84, 84, 84] 85 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 329 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581228 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581228 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581228/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581228 Building REAL300025581229 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581229' /scratch/stefan/7787361/working/building/REAL300025581229 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581229 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581229/0 /scratch/stefan/7787361/working/building/REAL300025581229 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/735 `/scratch/stefan/7787361/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581229 none COC1=CC=C(OC(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 196, 115, 35, 111, 112, 35, 36, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 115, 115, 111, 115, 112, 115, 35, 8, 8, 8, 8, 201, 201] 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: 576 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581229 none COC1=CC=C(OC(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 26, 26, 26, 55, 55, 55, 115, 115, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 55, 115, 115, 115, 115, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 593 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581229 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581229 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581229/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581229 Building REAL300025581230 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581230' /scratch/stefan/7787361/working/building/REAL300025581230 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581230 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581230/0 /scratch/stefan/7787361/working/building/REAL300025581230 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/736 `/scratch/stefan/7787361/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1) `REAL300025581230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581230 none CC(C)CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 4, 1, 4, 15, 15, 15, 71, 87, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 15, 71, 71, 87, 87, 1, 1, 1, 1] 201 rigid atoms, others: [4, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 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: 539 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581230 none CC(C)CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 190, 73, 73, 73, 20, 8, 1, 1, 1, 1, 1, 1, 1, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 72, 20, 20, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 816 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581230 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581230 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581230/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581230 Building REAL300025581231 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581231' /scratch/stefan/7787361/working/building/REAL300025581231 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581231 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581231/0 /scratch/stefan/7787361/working/building/REAL300025581231 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/737 `/scratch/stefan/7787361/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2NC(=O)N(CC(F)(F)F)C2=C1) `REAL300025581231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581231 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2NC(=O)N(CC(F)(F)F)C2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 49, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 5, 29, 29, 49, 49, 1, 1, 1, 2, 2, 1] 201 rigid atoms, others: [32, 1, 36, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 329 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581231 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2NC(=O)N(CC(F)(F)F)C2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 19, 8, 1, 1, 1, 1, 1, 1, 1, 59, 121, 121, 121, 121, 121, 121, 121, 121, 201, 201, 201, 201, 121, 121, 58, 19, 19, 8, 8, 121, 121, 121, 201, 201, 121] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 776 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581231 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581231 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581231/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581231 Building REAL300025581232 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581232' /scratch/stefan/7787361/working/building/REAL300025581232 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581232 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581232/0 /scratch/stefan/7787361/working/building/REAL300025581232 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/738 `/scratch/stefan/7787361/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21) `REAL300025581232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581232 none CC(C)N1C(=O)NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 85, 85, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 23, 23, 8, 8, 201] 201 rigid atoms, others: [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]) total number of confs: 440 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581232 none CC(C)N1C(=O)NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 51, 201, 201, 201, 201, 201, 1, 1, 5, 5, 5, 4, 4, 4, 4, 1, 1, 1, 5, 29, 29, 51, 51, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 39, 33, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581232 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581232 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581232/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581232 Building REAL300025581233 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581233' /scratch/stefan/7787361/working/building/REAL300025581233 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581233 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581233/0 /scratch/stefan/7787361/working/building/REAL300025581233 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/739 `/scratch/stefan/7787361/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=C(Cl)C=CC=C1Br)NCCC1=NC(=O)O[N-]1) `REAL300025581233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581233 none O=C(CC1=C(Cl)C=CC=C1Br)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 16, 1, 1, 1, 1, 17, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 121, 201, 201, 201, 201, 201, 201, 201, 18, 8, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 201, 31, 18, 18, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 604 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581233 none O=C(CC1=C(Cl)C=CC=C1Br)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 16, 1, 1, 1, 1, 17, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 124, 124, 201, 201, 201, 201, 201, 2, 2, 1, 1, 1, 24, 124, 124, 124, 124] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581233 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581233 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581233/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581233 Building REAL300025581234 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581234' /scratch/stefan/7787361/working/building/REAL300025581234 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581234 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581234/0 /scratch/stefan/7787361/working/building/REAL300025581234 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/740 `/scratch/stefan/7787361/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1Cl) `REAL300025581234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581234 none COC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 165, 165, 165, 165, 165, 117, 31, 31, 31, 13, 7, 1, 1, 1, 1, 1, 1, 1, 165, 165, 201, 201, 201, 165, 165, 165, 117, 117, 31, 13, 13, 7, 7] 201 rigid atoms, others: [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: 591 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581234 none COC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 5, 33, 33, 33, 96, 96, 165, 165, 165, 165, 165, 1, 1, 4, 4, 4, 1, 1, 1, 5, 5, 33, 96, 96, 96, 96] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20, 24, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 503 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581234 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581234 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581234/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581234 Building REAL300025581235 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581235' /scratch/stefan/7787361/working/building/REAL300025581235 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581235 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581235/0 /scratch/stefan/7787361/working/building/REAL300025581235 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/741 `/scratch/stefan/7787361/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C(F)(F)F)CCCCC1) `REAL300025581235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581235 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(F)(F)F)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 15, 15, 15, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 18, 32, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 85 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581235 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(F)(F)F)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 15, 15, 15, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 24, 8, 1, 1, 1, 1, 1, 1, 1, 69, 85, 85, 85, 85, 85, 85, 85, 85, 85, 69, 25, 24, 8, 8, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85] 85 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581235 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581235 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581235/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581235 Building REAL300025581236 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581236' /scratch/stefan/7787361/working/building/REAL300025581236 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581236 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581236/0 /scratch/stefan/7787361/working/building/REAL300025581236 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/742 `/scratch/stefan/7787361/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(OC1=CC=C(Br)C=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581236 none CC(C)(OC1=CC=C(Br)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 37, 126, 121, 201, 201, 201, 201, 201, 201, 201, 38, 38, 8, 8, 1, 1, 1, 1, 1, 1, 1, 129, 129, 126, 129, 126, 129, 201, 201, 201, 201, 37, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 608 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581236 none CC(C)(OC1=CC=C(Br)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 15, 1, 1, 1, 1, 1, 1, 1, 1, 15, 51, 51, 51, 112, 112, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 51, 112, 112, 112, 112] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 584 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581236 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581236 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581236/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581236 Building REAL300025581237 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581237' /scratch/stefan/7787361/working/building/REAL300025581237 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581237 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581237/0 /scratch/stefan/7787361/working/building/REAL300025581237 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/743 `/scratch/stefan/7787361/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NCCC1=NC(=O)O[N-]1)N(C)C(=O)OC(C)(C)C) `REAL300025581237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581237 none CCC(C(=O)NCCC1=NC(=O)O[N-]1)N(C)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 92, 39, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 94, 130, 130, 161, 161, 200, 200, 200, 200, 109, 109, 109, 109, 109, 94, 38, 8, 8, 8, 8, 130, 130, 130, 200, 200, 200, 200, 200, 200, 200, 200, 200] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 770 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581237 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581237 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581237/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581237 Building REAL300025581238 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581238' /scratch/stefan/7787361/working/building/REAL300025581238 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581238 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581238/0 /scratch/stefan/7787361/working/building/REAL300025581238 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/744 `/scratch/stefan/7787361/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)(F)F)N=C2CCCCN21) `REAL300025581238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581238 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)(F)F)N=C2CCCCN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 8, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 1, 8, 8, 40, 59, 131, 131, 131, 131, 131, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 40, 40, 59, 59, 1, 1, 1, 1, 1, 1, 1, 1] 131 rigid atoms, others: [32, 1, 34, 35, 36, 33, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 24, 25, 26, 27, 28]) total number of confs: 356 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581238 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)(F)F)N=C2CCCCN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 8, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [66, 66, 22, 8, 1, 1, 1, 1, 1, 1, 1, 66, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 66, 22, 22, 8, 8, 131, 131, 131, 131, 131, 131, 131, 131] 131 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581238 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581238 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581238/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581238 Building REAL300025581239 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581239' /scratch/stefan/7787361/working/building/REAL300025581239 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581239 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581239/0 /scratch/stefan/7787361/working/building/REAL300025581239 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/745 `/scratch/stefan/7787361/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](CC(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581239 none CC(C)(C)OC(=O)N1CC[C@H](CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 189, 157, 189, 157, 157, 157, 112, 157, 36, 36, 36, 8, 8, 1, 1, 1, 1, 1, 1, 1, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 157, 157, 157, 119, 119, 35, 8, 8, 8, 8, 157, 157] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 718 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581239 none CC(C)(C)OC(=O)N1CC[C@H](CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 31, 31, 31, 85, 85, 157, 157, 157, 157, 157, 1, 6, 6, 6, 5, 5, 5, 6, 6, 6, 1, 1, 1, 1, 6, 6, 31, 85, 85, 85, 85, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 45, 46, 24, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581239 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581239 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581239/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581239 Building REAL300025581240 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581240' /scratch/stefan/7787361/working/building/REAL300025581240 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581240 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581240/0 /scratch/stefan/7787361/working/building/REAL300025581240 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/746 `/scratch/stefan/7787361/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(Br)C=C1F)NCCC1=NC(=O)O[N-]1) `REAL300025581240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581240 none O=C(CC1=CC=C(Br)C=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 17, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 124, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 124, 124, 201, 201, 201, 34, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 585 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581240 none O=C(CC1=CC=C(Br)C=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 17, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 112, 114, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 35, 112, 112, 114, 114] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 587 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581240 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581240 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581240/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581240 Building REAL300025581241 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581241' /scratch/stefan/7787361/working/building/REAL300025581241 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581241 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581241/0 /scratch/stefan/7787361/working/building/REAL300025581241 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/747 `/scratch/stefan/7787361/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(N2C=CN=N2)=CC=C1F) `REAL300025581241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581241 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(N2C=CN=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 7, 32, 32, 106, 112, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 32, 106, 106, 112, 112, 7, 1, 1, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 540 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581241 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(N2C=CN=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 13, 63, 75, 156, 156, 156, 156, 156, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 1, 13, 63, 63, 75, 75, 1, 7, 7, 1, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 19, 20, 21, 22, 28, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 423 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581241 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(N2C=CN=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 19, 8, 1, 1, 1, 1, 1, 1, 1, 65, 156, 156, 156, 201, 201, 201, 201, 156, 156, 156, 156, 65, 19, 19, 8, 8, 156, 201, 201, 156, 156] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 424 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581241 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581241 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581241/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581241 Building REAL300025581242 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581242' /scratch/stefan/7787361/working/building/REAL300025581242 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581242 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581242/0 /scratch/stefan/7787361/working/building/REAL300025581242 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/748 `/scratch/stefan/7787361/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(N2C=NN=N2)CCOCC1) `REAL300025581242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581242 none O=C(NCCC1=NC(=O)O[N-]1)C1(N2C=NN=N2)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 8, 1, 8, 8, 8, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 5, 37, 37, 113, 122, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 37, 113, 113, 122, 122, 1, 5, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 589 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581242 none O=C(NCCC1=NC(=O)O[N-]1)C1(N2C=NN=N2)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 8, 1, 8, 8, 8, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 63, 72, 166, 166, 166, 166, 166, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 13, 63, 63, 72, 72, 5, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581242 none O=C(NCCC1=NC(=O)O[N-]1)C1(N2C=NN=N2)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 8, 1, 8, 8, 8, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 17, 8, 1, 1, 1, 1, 1, 1, 1, 62, 166, 201, 201, 201, 201, 166, 166, 166, 166, 166, 62, 17, 17, 8, 8, 201, 166, 166, 166, 166, 166, 166, 166, 166] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 566 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581242 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581242 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581242/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581242 Building REAL300025581243 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581243' /scratch/stefan/7787361/working/building/REAL300025581243 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581243 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581243/0 /scratch/stefan/7787361/working/building/REAL300025581243 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/749 `/scratch/stefan/7787361/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC(C)C) `REAL300025581243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581243 none CC(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 96, 190, 96, 96, 44, 44, 44, 16, 8, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 170, 189, 189, 190, 190, 190, 96, 44, 16, 16, 8, 8, 96, 96, 189, 189, 189, 189, 189, 189, 189] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 790 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581243 none CC(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 1, 1, 5, 5, 5, 23, 27, 96, 96, 96, 96, 96, 1, 1, 1, 1, 5, 9, 9, 7, 7, 7, 1, 5, 23, 23, 27, 27, 1, 1, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 17, 18, 19, 20, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 233 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581243 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581243 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581243/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581243 Building REAL300025581244 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581244' /scratch/stefan/7787361/working/building/REAL300025581244 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581244 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581244/0 /scratch/stefan/7787361/working/building/REAL300025581244 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/750 `/scratch/stefan/7787361/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(CCOCC2)C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581244 none CC(C)(C)OC(=O)N1CC2(CCOCC2)C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 134, 116, 79, 116, 79, 79, 79, 79, 79, 79, 79, 79, 63, 63, 63, 23, 8, 1, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134, 134, 134, 134, 134, 134, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 63, 24, 24, 8, 8] 134 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 460 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581244 none CC(C)(C)OC(=O)N1CC2(CCOCC2)C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 11, 13, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 26, 79, 79, 79, 79, 79, 14, 14, 14, 13, 13, 13, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 16, 16, 26, 26] 134 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581244 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581244 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581244/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581244 Building REAL300025581245 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581245' /scratch/stefan/7787361/working/building/REAL300025581245 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581245 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581245/0 /scratch/stefan/7787361/working/building/REAL300025581245 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/751 `/scratch/stefan/7787361/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C2C[N@H+](C)CCC2C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025581245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581245 none CN1C=C(C2C[N@H+](C)CCC2C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 53, 53, 53, 53, 53, 53, 53, 53, 39, 39, 39, 15, 9, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 39, 15, 15, 9, 9, 75] 75 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 228 number of broken/clashed sets: 75 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581245 none CN1C=C(C2C[N@H+](C)CCC2C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 17, 21, 53, 53, 53, 53, 53, 8, 8, 8, 8, 8, 8, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 17, 17, 21, 21, 8] 75 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 37, 35, 39, 36, 38, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 40, 41, 42, 43, 44, 45]) total number of confs: 145 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581245 none CN1C=C(C2C[N@H+](C)CCC2C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 34, 37, 75, 75, 75, 75, 75, 1, 1, 2, 2, 2, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 34, 34, 37, 37, 1] 75 rigid atoms, others: [0, 1, 2, 3, 4, 45, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 214 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581245 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581245/1 /scratch/stefan/7787361/working/building/REAL300025581245 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/752 `/scratch/stefan/7787361/working/3D/752' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C2C[N@@H+](C)CCC2C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025581245.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581245 none CN1C=C(C2C[N@@H+](C)CCC2C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 136, 136, 136, 136, 136, 136, 136, 136, 74, 74, 74, 17, 9, 1, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 179, 179, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 74, 17, 17, 9, 9, 179] 179 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 512 number of broken/clashed sets: 179 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581245 none CN1C=C(C2C[N@@H+](C)CCC2C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 32, 43, 136, 136, 136, 136, 136, 7, 7, 8, 8, 8, 7, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 6, 32, 32, 43, 43, 7] 179 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 37, 35, 39, 36, 38, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 40, 41, 42, 43, 44, 45]) total number of confs: 320 number of broken/clashed sets: 179 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581245 none CN1C=C(C2C[N@@H+](C)CCC2C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 84, 99, 179, 179, 179, 179, 179, 1, 1, 2, 2, 2, 1, 7, 7, 7, 8, 8, 8, 7, 7, 7, 7, 7, 23, 84, 84, 99, 99, 1] 179 rigid atoms, others: [0, 1, 2, 3, 4, 45, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 537 number of broken/clashed sets: 179 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581245 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581245 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581245/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581245/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581245 Building REAL300025581246 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581246' /scratch/stefan/7787361/working/building/REAL300025581246 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581246 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581246/0 /scratch/stefan/7787361/working/building/REAL300025581246 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/753 `/scratch/stefan/7787361/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@@H+]1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CN(C)N=C2)C1) `REAL300025581246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581246 none CC(C)[N@@H+]1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CN(C)N=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 30, 33, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 11, 30, 30, 33, 33, 7, 1, 2, 2, 2, 1, 7, 7] 67 rigid atoms, others: [45, 49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 50, 51]) total number of confs: 193 number of broken/clashed sets: 67 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581246 none CC(C)[N@@H+]1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CN(C)N=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 46, 46, 46, 46, 46, 46, 36, 36, 36, 14, 9, 1, 1, 1, 1, 1, 1, 1, 46, 46, 67, 67, 67, 67, 67, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 36, 14, 14, 9, 9, 46, 67, 67, 67, 67, 67, 46, 46] 67 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 204 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581246 none CC(C)[N@@H+]1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CN(C)N=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 18, 46, 46, 46, 46, 46, 1, 1, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 4, 14, 14, 18, 18, 1, 7, 7, 7, 7, 7, 1, 1] 67 rigid atoms, others: [19, 1, 34, 3, 4, 5, 6, 7, 8, 44, 50, 35, 20, 36, 26, 38, 51, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 130 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581246 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581246/1 /scratch/stefan/7787361/working/building/REAL300025581246 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/754 `/scratch/stefan/7787361/working/3D/754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@H+]1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CN(C)N=C2)C1) `REAL300025581246.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581246 none CC(C)[N@H+]1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CN(C)N=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 7, 8, 7, 7, 7, 7, 7, 7, 25, 25, 25, 76, 86, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 25, 76, 76, 86, 86, 7, 1, 2, 2, 2, 1, 7, 7] 159 rigid atoms, others: [45, 49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 50, 51]) total number of confs: 469 number of broken/clashed sets: 159 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581246 none CC(C)[N@H+]1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CN(C)N=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [118, 118, 118, 118, 118, 118, 118, 70, 70, 70, 17, 9, 1, 1, 1, 1, 1, 1, 1, 118, 118, 159, 159, 159, 159, 159, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 70, 17, 17, 9, 9, 118, 159, 159, 159, 159, 159, 118, 118] 159 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 458 number of broken/clashed sets: 159 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581246 none CC(C)[N@H+]1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CN(C)N=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 34, 45, 118, 118, 118, 118, 118, 1, 1, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 7, 34, 34, 45, 45, 1, 7, 8, 8, 8, 7, 1, 1] 159 rigid atoms, others: [19, 1, 34, 3, 4, 5, 6, 7, 8, 44, 50, 35, 20, 36, 26, 38, 51, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 305 number of broken/clashed sets: 159 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581246 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581246 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581246/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581246/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581246 Building REAL300025581247 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581247' /scratch/stefan/7787361/working/building/REAL300025581247 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581247 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581247/0 /scratch/stefan/7787361/working/building/REAL300025581247 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/755 `/scratch/stefan/7787361/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(Cl)=C1Cl) `REAL300025581247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581247 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 16, 1, 16, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 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: [7, 1, 7, 7, 39, 67, 163, 163, 163, 163, 163, 1, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 67, 67, 1, 1] 163 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 435 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581247 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 16, 1, 16, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 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: [97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 97, 163, 163, 163, 163, 163, 163, 163, 97, 24, 24, 8, 8, 163, 163] 163 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 393 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581247 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581247 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581247/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581247 Building REAL300025581248 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581248' /scratch/stefan/7787361/working/building/REAL300025581248 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581248 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581248/0 /scratch/stefan/7787361/working/building/REAL300025581248 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/756 `/scratch/stefan/7787361/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C(F)(F)F)=CNC1=O) `REAL300025581248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581248 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C(F)(F)F)=CNC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 74, 114, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 13, 74, 74, 114, 114, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 18, 19, 20, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 625 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581248 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C(F)(F)F)=CNC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 25, 25, 8, 8, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581248 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581248 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581248/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581248 Building REAL300025581249 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581249' /scratch/stefan/7787361/working/building/REAL300025581249 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581249 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581249/0 /scratch/stefan/7787361/working/building/REAL300025581249 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/757 `/scratch/stefan/7787361/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CNC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025581249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581249 none CC(=O)NC1=CNC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 147, 147, 147, 147, 147, 147, 67, 67, 67, 20, 8, 1, 1, 1, 1, 1, 1, 1, 147, 201, 201, 201, 201, 147, 147, 67, 20, 20, 8, 8, 147] 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]) total number of confs: 540 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581249 none CC(=O)NC1=CNC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 44, 56, 147, 147, 147, 147, 147, 1, 4, 4, 4, 4, 1, 1, 12, 44, 44, 56, 56, 1] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 9, 10, 21, 26, 27] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581249 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581249 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581249/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581249 Building REAL300025581250 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581250' /scratch/stefan/7787361/working/building/REAL300025581250 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581250 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581250/0 /scratch/stefan/7787361/working/building/REAL300025581250 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/758 `/scratch/stefan/7787361/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=N[N-]N=N2)C=N1) `REAL300025581250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581250 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=N[N-]N=N2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [19, 4, 19, 19, 42, 44, 65, 65, 65, 65, 65, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 19, 42, 42, 44, 44, 5, 5, 5] 65 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 207 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581250 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=N[N-]N=N2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [7, 1, 7, 7, 27, 32, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 7, 27, 27, 32, 32, 1, 1, 1] 65 rigid atoms, others: [1, 11, 12, 13, 14, 15, 20, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26]) total number of confs: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581250 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=N[N-]N=N2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [40, 40, 18, 8, 1, 1, 1, 1, 1, 1, 1, 40, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 39, 18, 18, 8, 8, 65, 65, 65] 65 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581250 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581250/1 /scratch/stefan/7787361/working/building/REAL300025581250 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/759 `/scratch/stefan/7787361/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=NN=N[N-]2)C=N1) `REAL300025581250.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581250 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=NN=N[N-]2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [19, 4, 19, 19, 44, 46, 65, 65, 65, 65, 65, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 19, 43, 43, 46, 46, 5, 5, 5] 65 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 208 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581250 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=NN=N[N-]2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [7, 1, 7, 7, 28, 32, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 7, 27, 27, 32, 32, 1, 1, 1] 65 rigid atoms, others: [1, 11, 12, 13, 14, 15, 20, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581250 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=NN=N[N-]2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [40, 39, 18, 8, 1, 1, 1, 1, 1, 1, 1, 40, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 39, 18, 18, 8, 8, 65, 65, 65] 65 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581250 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581250 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581250/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581250/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581250 Building REAL300025581251 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581251' /scratch/stefan/7787361/working/building/REAL300025581251 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581251 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581251/0 /scratch/stefan/7787361/working/building/REAL300025581251 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/760 `/scratch/stefan/7787361/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=N1) `REAL300025581251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581251 none CN1C=CC(NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 186, 120, 120, 120, 120, 47, 47, 47, 17, 8, 1, 1, 1, 1, 1, 1, 1, 120, 120, 201, 201, 201, 201, 201, 201, 186, 120, 120, 47, 17, 17, 8, 8, 120, 120] 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]) total number of confs: 517 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581251 none CN1C=CC(NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 33, 120, 120, 120, 120, 120, 1, 1, 14, 14, 14, 14, 14, 14, 6, 1, 1, 5, 29, 29, 33, 33, 1, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 21, 22, 38, 37, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581251 none CN1C=CC(NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 14, 14, 9, 11, 45, 45, 45, 123, 123, 201, 201, 201, 201, 201, 14, 14, 1, 2, 2, 2, 1, 1, 9, 14, 14, 45, 123, 123, 123, 123, 14, 14] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581251 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581251 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581251/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581251 Building REAL300025581252 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581252' /scratch/stefan/7787361/working/building/REAL300025581252 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581252 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581252/0 /scratch/stefan/7787361/working/building/REAL300025581252 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/761 `/scratch/stefan/7787361/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCN(CC(F)(F)F)CC1)NCCC1=NC(=O)O[N-]1) `REAL300025581252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581252 none O=C(CC1CCN(CC(F)(F)F)CC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 99, 153, 153, 153, 153, 201, 201, 201, 201, 153, 153, 16, 8, 1, 1, 1, 1, 1, 1, 1, 99, 99, 153, 153, 153, 153, 153, 201, 201, 153, 153, 153, 153, 43, 16, 16, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 880 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581252 none O=C(CC1CCN(CC(F)(F)F)CC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 22, 22, 66, 69, 153, 153, 153, 153, 153, 5, 5, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 22, 66, 66, 69, 69] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 12, 13, 34, 35, 25, 26, 27, 28, 29] set([0, 1, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 411 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581252 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581252 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581252/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581252 Building REAL300025581253 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581253' /scratch/stefan/7787361/working/building/REAL300025581253 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581253 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581253/0 /scratch/stefan/7787361/working/building/REAL300025581253 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/762 `/scratch/stefan/7787361/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1CCC(C2OCCO2)O1)NCCC1=NC(=O)O[N-]1) `REAL300025581253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581253 none O=C(CCC1CCC(C2OCCO2)O1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 12, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 23, 23, 24, 24, 24, 24, 35, 35, 35, 35, 24, 13, 8, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 35, 35, 35, 35, 35, 22, 13, 13, 8, 8] 35 rigid atoms, others: [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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581253 none O=C(CCC1CCC(C2OCCO2)O1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 12, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 12, 12, 20, 20, 35, 35, 35, 35, 35, 12, 12, 12, 12, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 12, 20, 20, 20, 20] 35 rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581253 none O=C(CCC1CCC(C2OCCO2)O1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 12, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 4, 4, 8, 8, 24, 24, 24, 24, 24, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 4, 8, 8, 8, 8] 35 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 13, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581253 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581253 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581253/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581253 Building REAL300025581254 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581254' /scratch/stefan/7787361/working/building/REAL300025581254 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581254 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581254/0 /scratch/stefan/7787361/working/building/REAL300025581254 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/763 `/scratch/stefan/7787361/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C(I)=NN1) `REAL300025581254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581254 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C(I)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'I', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 18, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 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, 95, 95, 95, 21, 8, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 177, 177, 95, 21, 22, 8, 8, 177] 177 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 432 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581254 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C(I)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'I', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 18, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 5, 5, 5, 33, 60, 177, 177, 177, 177, 177, 1, 1, 1, 1, 2, 2, 2, 5, 33, 33, 60, 60, 1] 177 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 429 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581254 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581254 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581254/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581254 Building REAL300025581255 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581255' /scratch/stefan/7787361/working/building/REAL300025581255 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581255 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581255/0 /scratch/stefan/7787361/working/building/REAL300025581255 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/764 `/scratch/stefan/7787361/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(NN2C=CN=C2)C=C1) `REAL300025581255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581255 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(NN2C=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 53, 53, 138, 144, 201, 201, 201, 201, 201, 9, 29, 29, 7, 1, 1, 1, 1, 1, 1, 29, 29, 53, 138, 138, 144, 144, 29, 29, 7, 1, 1, 1, 29, 29] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 31] 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, 34, 35]) total number of confs: 683 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581255 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(NN2C=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 18, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 11, 29, 29, 29, 29, 1, 1, 3, 15, 15, 18, 18, 1, 1, 11, 29, 29, 29, 1, 1] 201 rigid atoms, others: [1, 34, 35, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581255 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(NN2C=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 47, 70, 70, 47, 47, 115, 201, 201, 201, 201, 70, 70, 47, 19, 19, 8, 8, 70, 70, 115, 201, 201, 201, 70, 70] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 651 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581255 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581255 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581255/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581255 Building REAL300025581256 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581256' /scratch/stefan/7787361/working/building/REAL300025581256 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581256 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581256/0 /scratch/stefan/7787361/working/building/REAL300025581256 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/765 `/scratch/stefan/7787361/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NN=NN1C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025581256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581256 none NC1=NN=NN1C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 135, 135, 135, 135, 135, 58, 58, 58, 17, 8, 1, 1, 1, 1, 1, 1, 1, 135, 201, 201, 135, 135, 135, 58, 17, 17, 8, 8, 135] 201 rigid atoms, others: [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]) total number of confs: 416 number of broken/clashed sets: 176 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581256 none NC1=NN=NN1C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 35, 135, 135, 135, 135, 135, 1, 9, 9, 1, 1, 1, 5, 29, 29, 35, 35, 1] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 11, 22, 25, 26, 27] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 272 number of broken/clashed sets: 176 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581256 none NC1=NN=NN1C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 24, 24, 24, 90, 98, 201, 201, 201, 201, 201, 9, 1, 1, 9, 9, 9, 24, 90, 90, 98, 98, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 529 number of broken/clashed sets: 176 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581256 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581256 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581256/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581256 Building REAL300025581257 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581257' /scratch/stefan/7787361/working/building/REAL300025581257 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581257 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581257/0 /scratch/stefan/7787361/working/building/REAL300025581257 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/766 `/scratch/stefan/7787361/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(NC2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)=N1) `REAL300025581257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581257 none CC1=CC=NC(NC2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 134, 201, 201, 134, 76, 76, 76, 76, 76, 56, 56, 56, 17, 8, 1, 1, 1, 1, 1, 1, 1, 76, 201, 201, 201, 201, 134, 201, 134, 76, 76, 76, 56, 17, 17, 8, 8, 76] 201 rigid atoms, others: [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]) total number of confs: 737 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581257 none CC1=CC=NC(NC2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 9, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 17, 76, 76, 76, 76, 76, 1, 31, 31, 31, 31, 9, 31, 9, 1, 1, 1, 3, 13, 13, 17, 17, 1] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581257 none CC1=CC=NC(NC2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 31, 31, 31, 31, 31, 49, 49, 49, 115, 117, 201, 201, 201, 201, 201, 31, 1, 2, 2, 2, 1, 1, 7, 31, 31, 31, 49, 115, 115, 117, 117, 31] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 559 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581257 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581257 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581257/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581257 Building REAL300025581258 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581258' /scratch/stefan/7787361/working/building/REAL300025581258 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581258 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581258/0 /scratch/stefan/7787361/working/building/REAL300025581258 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/767 `/scratch/stefan/7787361/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC=C(Br)C=C1) `REAL300025581258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581258 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 33, 33, 114, 118, 201, 201, 201, 201, 201, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 33, 114, 114, 118, 118, 1, 1, 1, 1] 201 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25]) total number of confs: 580 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581258 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 1, 64, 160, 160, 160, 201, 201, 160, 176, 201, 201, 64, 19, 19, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 841 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581258 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581258 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581258/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581258 Building REAL300025581259 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581259' /scratch/stefan/7787361/working/building/REAL300025581259 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581259 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581259/0 /scratch/stefan/7787361/working/building/REAL300025581259 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/768 `/scratch/stefan/7787361/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CN2C=C(C(F)(F)F)N=C12) `REAL300025581259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581259 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CN2C=C(C(F)(F)F)N=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 67, 92, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 12, 67, 67, 92, 92, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 546 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581259 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CN2C=C(C(F)(F)F)N=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 23, 8, 1, 1, 1, 1, 1, 1, 1, 102, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 23, 23, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581259 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581259 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581259/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581259 Building REAL300025581260 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581260' /scratch/stefan/7787361/working/building/REAL300025581260 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581260 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581260/0 /scratch/stefan/7787361/working/building/REAL300025581260 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/769 `/scratch/stefan/7787361/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1=CN(C)N=C1) `REAL300025581260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581260 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 31, 31, 31, 101, 110, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 31, 101, 101, 110, 110, 5, 5, 5, 1, 2, 2, 2, 1] 201 rigid atoms, others: [36, 40, 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, 37, 38, 39]) total number of confs: 570 number of broken/clashed sets: 41 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581260 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 57, 57, 57, 21, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 201, 201, 201, 201, 201, 128, 128, 128, 128, 57, 21, 21, 8, 8, 128, 128, 128, 201, 201, 201, 201, 201] 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, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 441 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581260 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 38, 44, 128, 128, 128, 128, 128, 1, 1, 1, 1, 5, 5, 5, 5, 5, 2, 2, 2, 1, 10, 38, 38, 44, 44, 2, 2, 2, 5, 5, 5, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 300 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581260 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581260 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581260/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581260 Building REAL300025581261 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581261' /scratch/stefan/7787361/working/building/REAL300025581261 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581261 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581261/0 /scratch/stefan/7787361/working/building/REAL300025581261 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/770 `/scratch/stefan/7787361/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC2=CC=CC=C21) `REAL300025581261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581261 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 57, 91, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 57, 57, 91, 91, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 557 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581261 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 23, 8, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 23, 23, 8, 8, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581261 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581261 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581261/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581261 Building REAL300025581262 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581262' /scratch/stefan/7787361/working/building/REAL300025581262 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581262 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581262/0 /scratch/stefan/7787361/working/building/REAL300025581262 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/771 `/scratch/stefan/7787361/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(NCC2=CC=CC=N2)=C1) `REAL300025581262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581262 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(NCC2=CC=CC=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 32, 61, 61, 130, 131, 201, 201, 201, 201, 201, 32, 32, 32, 32, 17, 8, 1, 1, 1, 1, 1, 1, 1, 32, 61, 130, 130, 131, 131, 32, 32, 32, 17, 8, 8, 1, 1, 1, 1, 32] 201 rigid atoms, others: [36, 37, 38, 39, 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, 40]) total number of confs: 636 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581262 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(NCC2=CC=CC=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 21, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 7, 16, 32, 32, 32, 32, 32, 1, 5, 19, 19, 21, 21, 1, 1, 1, 7, 16, 16, 32, 32, 32, 32, 1] 201 rigid atoms, others: [32, 1, 40, 11, 12, 13, 14, 15, 16, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 216 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581262 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(NCC2=CC=CC=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 16, 8, 1, 1, 1, 1, 1, 1, 1, 38, 66, 66, 66, 66, 66, 137, 150, 201, 201, 201, 201, 201, 66, 38, 16, 16, 8, 8, 66, 66, 66, 137, 150, 150, 201, 201, 201, 201, 66] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 562 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581262 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581262 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581262/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581262 Building REAL300025581263 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581263' /scratch/stefan/7787361/working/building/REAL300025581263 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581263 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581263/0 /scratch/stefan/7787361/working/building/REAL300025581263 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/772 `/scratch/stefan/7787361/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Br)=N1) `REAL300025581263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581263 none NC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Br)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Br', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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, 50, 50, 50, 20, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 133, 133, 50, 20, 20, 8, 8, 133] 133 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]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581263 none NC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Br)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Br', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 5, 5, 5, 30, 51, 133, 133, 133, 133, 133, 1, 1, 1, 1, 2, 2, 1, 5, 30, 30, 51, 51, 1] 133 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 21, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581263 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581263 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581263/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581263 Building REAL300025581264 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581264' /scratch/stefan/7787361/working/building/REAL300025581264 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581264 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581264/0 /scratch/stefan/7787361/working/building/REAL300025581264 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/773 `/scratch/stefan/7787361/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C2=CC=CC=C2SC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1) `REAL300025581264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581264 none O=C(CN1C2=CC=CC=C2SC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', '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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 23, 8, 1, 1, 1, 1, 1, 1, 1, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 73, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 634 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581264 none O=C(CN1C2=CC=CC=C2SC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', '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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 81, 97, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 21, 81, 81, 97, 97] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 570 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581264 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581264 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581264/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581264 Building REAL300025581265 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581265' /scratch/stefan/7787361/working/building/REAL300025581265 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581265 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581265/0 /scratch/stefan/7787361/working/building/REAL300025581265 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/774 `/scratch/stefan/7787361/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C2C(=O)C(C(=O)NCCC3=NC(=O)O[N-]3)=CNC2=C1) `REAL300025581265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581265 none COC1=CC(OC)=C2C(=O)C(C(=O)NCCC3=NC(=O)O[N-]3)=CNC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 159, 159, 159, 159, 159, 201, 159, 159, 159, 73, 73, 73, 22, 8, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 201, 201, 201, 159, 201, 201, 201, 72, 22, 22, 8, 8, 159, 159, 159] 201 rigid atoms, others: [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: 522 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581265 none COC1=CC(OC)=C2C(=O)C(C(=O)NCCC3=NC(=O)O[N-]3)=CNC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 4, 1, 1, 1, 1, 1, 12, 12, 12, 49, 62, 159, 159, 159, 159, 159, 1, 1, 1, 1, 3, 3, 3, 1, 4, 4, 4, 12, 49, 49, 62, 62, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 7, 8, 9, 10, 11, 40, 22, 23, 24, 25, 29, 39] set([0, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581265 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581265/1 /scratch/stefan/7787361/working/building/REAL300025581265 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/775 `/scratch/stefan/7787361/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C2C(=O)C(C(=O)NCCC3=NC(=O)O[N-]3)=C[N-]C2=C1) `REAL300025581265.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581265 none COC1=CC(OC)=C2C(=O)C(C(=O)NCCC3=NC(=O)O[N-]3)=C[N-]C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 167, 167, 167, 167, 167, 181, 167, 167, 167, 62, 62, 62, 14, 8, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 181, 181, 181, 167, 181, 181, 181, 61, 15, 15, 8, 8, 167, 167] 181 rigid atoms, others: [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]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581265 none COC1=CC(OC)=C2C(=O)C(C(=O)NCCC3=NC(=O)O[N-]3)=C[N-]C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 1, 1, 1, 1, 4, 1, 1, 1, 1, 1, 13, 13, 13, 65, 69, 167, 167, 167, 167, 167, 1, 1, 1, 1, 3, 3, 3, 1, 4, 4, 4, 13, 65, 65, 69, 69, 1, 1] 181 rigid atoms, others: [1, 2, 3, 4, 5, 38, 7, 8, 9, 10, 11, 22, 23, 24, 25, 29, 39] set([0, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581265 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581265 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581265/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581265/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581265 Building REAL300025581266 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581266' /scratch/stefan/7787361/working/building/REAL300025581266 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581266 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581266/0 /scratch/stefan/7787361/working/building/REAL300025581266 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/776 `/scratch/stefan/7787361/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1NC(=O)C2=CC=CC=C21)NCCC1=NC(=O)O[N-]1) `REAL300025581266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581266 none O=C(CC1NC(=O)C2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 181, 201, 201, 201, 201, 201, 201, 201, 201, 201, 21, 8, 1, 1, 1, 1, 1, 1, 1, 181, 181, 201, 201, 201, 201, 201, 201, 70, 21, 21, 8, 8] 201 rigid atoms, others: [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: 739 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581266 none O=C(CC1NC(=O)C2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 101, 113, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 26, 101, 101, 113, 113] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29] set([0, 1, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581266 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581266 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581266/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581266 Building REAL300025581267 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581267' /scratch/stefan/7787361/working/building/REAL300025581267 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581267 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581267/0 /scratch/stefan/7787361/working/building/REAL300025581267 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/777 `/scratch/stefan/7787361/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581267 none CS(=O)(=O)N1CCC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 160, 201, 201, 160, 160, 160, 160, 62, 160, 62, 62, 17, 8, 1, 1, 1, 1, 1, 1, 1, 160, 201, 201, 201, 160, 160, 160, 160, 160, 160, 62, 17, 17, 8, 8, 160, 160] 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]) total number of confs: 724 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581267 none CS(=O)(=O)N1CCC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 57, 64, 160, 160, 160, 160, 160, 1, 7, 7, 7, 1, 1, 1, 1, 1, 1, 13, 57, 57, 64, 64, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 37, 21, 25, 26, 27, 28, 29, 30, 36] set([0, 32, 2, 3, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 34, 31]) total number of confs: 396 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581267 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581267 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581267/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581267 Building REAL300025581268 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581268' /scratch/stefan/7787361/working/building/REAL300025581268 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581268 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581268/0 /scratch/stefan/7787361/working/building/REAL300025581268 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/778 `/scratch/stefan/7787361/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1OC(F)F) `REAL300025581268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581268 none COC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 13, 13, 13, 9, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 9, 9, 5, 5, 15, 15] 15 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, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581268 none COC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 11, 11, 15, 15, 15, 15, 15, 1, 1, 1, 3, 5, 5, 2, 2, 2, 1, 1, 3, 3, 7, 11, 11, 11, 11, 1, 5] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 36, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581268 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581268 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581268/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581268 Building REAL300025581269 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581269' /scratch/stefan/7787361/working/building/REAL300025581269 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581269 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581269/0 /scratch/stefan/7787361/working/building/REAL300025581269 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/779 `/scratch/stefan/7787361/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1Br) `REAL300025581269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581269 none CC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 166, 121, 32, 32, 32, 15, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 121, 121, 32, 15, 15, 8, 8] 201 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]) total number of confs: 678 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581269 none CC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 35, 35, 35, 116, 116, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 6, 6, 35, 116, 116, 116, 116] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 23, 24, 25] set([32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581269 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581269 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581269/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581269 Building REAL300025581270 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581270' /scratch/stefan/7787361/working/building/REAL300025581270 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581270 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581270/0 /scratch/stefan/7787361/working/building/REAL300025581270 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/780 `/scratch/stefan/7787361/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(=O)N2CCOCC2)C=C1) `REAL300025581270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581270 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(=O)N2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 13, 35, 35, 121, 121, 201, 201, 201, 201, 201, 13, 19, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 35, 121, 121, 121, 121, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41]) total number of confs: 617 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581270 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(=O)N2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 17, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 11, 11, 19, 19, 19, 19, 19, 1, 1, 3, 15, 15, 17, 17, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [1, 40, 41, 11, 12, 13, 14, 15, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581270 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(=O)N2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 17, 8, 1, 1, 1, 1, 1, 1, 1, 40, 62, 62, 40, 40, 141, 141, 201, 201, 201, 201, 201, 62, 62, 40, 17, 17, 8, 8, 62, 62, 201, 201, 201, 201, 201, 201, 201, 201, 62, 62] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 630 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581270 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581270 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581270/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581270 Building REAL300025581271 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581271' /scratch/stefan/7787361/working/building/REAL300025581271 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581271 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581271/0 /scratch/stefan/7787361/working/building/REAL300025581271 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/781 `/scratch/stefan/7787361/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(CN2C=CN=N2)C=C1) `REAL300025581271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581271 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(CN2C=CN=N2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 8, 1, 1, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 13, 39, 39, 106, 108, 201, 201, 201, 201, 201, 13, 23, 23, 8, 1, 1, 1, 1, 1, 1, 23, 23, 39, 106, 106, 108, 108, 23, 23, 8, 8, 1, 1, 23, 23] 201 rigid atoms, others: [32, 33, 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, 34, 35]) total number of confs: 614 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581271 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(CN2C=CN=N2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 8, 1, 1, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 17, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 1, 1, 3, 15, 15, 17, 17, 1, 1, 7, 7, 23, 23, 1, 1] 201 rigid atoms, others: [1, 34, 35, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 182 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581271 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(CN2C=CN=N2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 8, 1, 1, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 17, 8, 1, 1, 1, 1, 1, 1, 1, 48, 79, 79, 54, 79, 148, 201, 201, 201, 201, 79, 79, 48, 17, 17, 8, 8, 79, 79, 148, 148, 201, 201, 79, 79] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 761 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581271 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581271 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581271/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581271 Building REAL300025581272 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581272' /scratch/stefan/7787361/working/building/REAL300025581272 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581272 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581272/0 /scratch/stefan/7787361/working/building/REAL300025581272 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/782 `/scratch/stefan/7787361/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC(F)(F)CC1) `REAL300025581272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581272 none CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 146, 89, 89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 146, 146, 146, 154, 154, 154, 154, 154, 89, 24, 24, 8, 8, 146, 146, 146, 146, 146, 146, 146, 146] 154 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 543 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581272 none CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 1, 1, 3, 3, 3, 19, 36, 146, 146, 146, 146, 146, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 19, 19, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1] 154 rigid atoms, others: [32, 1, 2, 3, 36, 37, 35, 33, 34, 14, 15, 16, 17, 18, 19, 20, 38, 31] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581272 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581272 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581272/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581272 Building REAL300025581273 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581273' /scratch/stefan/7787361/working/building/REAL300025581273 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581273 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581273/0 /scratch/stefan/7787361/working/building/REAL300025581273 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/783 `/scratch/stefan/7787361/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(F)(F)F)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581273 none CN1N=CC(C(F)(F)F)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 15, 15, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 92, 92, 92, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 91, 22, 22, 8, 8] 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]) total number of confs: 441 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581273 none CN1N=CC(C(F)(F)F)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 15, 15, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 73, 105, 201, 201, 201, 201, 201, 2, 2, 2, 1, 12, 73, 73, 105, 105] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 583 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581273 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581273 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581273/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581273 Building REAL300025581274 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581274' /scratch/stefan/7787361/working/building/REAL300025581274 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581274 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581274/0 /scratch/stefan/7787361/working/building/REAL300025581274 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/784 `/scratch/stefan/7787361/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1OCCO[C@@H]1C1=CC=CC=C1) `REAL300025581274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581274 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1OCCO[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 12, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 3, 8, 8, 33, 47, 127, 127, 127, 127, 127, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 33, 33, 47, 47, 3, 3, 3, 3, 1, 1, 1, 1, 1] 127 rigid atoms, others: [34, 35, 36, 37, 38, 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]) total number of confs: 312 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581274 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1OCCO[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 12, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 28, 43, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 6, 28, 28, 43, 43, 1, 1, 1, 1, 3, 3, 2, 3, 3] 127 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581274 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1OCCO[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 12, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [62, 62, 22, 9, 1, 1, 1, 1, 1, 1, 1, 62, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 62, 22, 22, 9, 9, 127, 127, 127, 127, 127, 127, 127, 127, 127] 127 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581274 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581274 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581274/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581274 Building REAL300025581275 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581275' /scratch/stefan/7787361/working/building/REAL300025581275 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581275 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581275/0 /scratch/stefan/7787361/working/building/REAL300025581275 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/785 `/scratch/stefan/7787361/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(C2=NNC=C2C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581275 none CC(C)(C)OC(=O)N1CCC(C2=NNC=C2C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 168, 116, 168, 116, 116, 116, 55, 55, 55, 55, 55, 28, 28, 28, 14, 7, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 116, 116, 116, 116, 55, 55, 28, 14, 14, 7, 7, 116, 116] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 598 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581275 none CC(C)(C)OC(=O)N1CCC(C2=NNC=C2C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 11, 6, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 23, 55, 55, 55, 55, 55, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 1, 1, 3, 19, 19, 23, 23, 6, 6] 201 rigid atoms, others: [43, 10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581275 none CC(C)(C)OC(=O)N1CCC(C2=NNC=C2C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 55, 56, 116, 116, 116, 116, 116, 1, 6, 6, 6, 5, 5, 5, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 13, 55, 55, 56, 56, 1, 1] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 40, 50, 41, 49, 27, 5] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581275 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581275/1 /scratch/stefan/7787361/working/building/REAL300025581275 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/786 `/scratch/stefan/7787361/working/3D/786' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(C2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=NN2)C1) `REAL300025581275.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581275 none CC(C)(C)OC(=O)N1CCC(C2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=NN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 149, 200, 149, 149, 149, 66, 66, 24, 24, 24, 12, 6, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 149, 149, 149, 24, 12, 12, 6, 6, 66, 66, 149, 149] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 599 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581275 none CC(C)(C)OC(=O)N1CCC(C2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=NN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 10, 5, 10, 5, 5, 5, 1, 1, 1, 1, 6, 6, 6, 28, 30, 66, 66, 66, 66, 66, 1, 1, 1, 5, 12, 12, 12, 11, 11, 11, 12, 12, 12, 5, 5, 5, 5, 5, 6, 28, 28, 30, 30, 1, 1, 5, 5] 201 rigid atoms, others: [10, 11, 12, 13, 47, 48, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581275 none CC(C)(C)OC(=O)N1CCC(C2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=NN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 74, 75, 149, 149, 149, 149, 149, 5, 5, 5, 1, 4, 4, 4, 3, 3, 3, 4, 4, 4, 1, 1, 1, 1, 1, 19, 74, 74, 75, 75, 5, 5, 1, 1] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 40, 50, 41, 49, 27, 5] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581275 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581275 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581275/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581275/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581275 Building REAL300025581276 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581276' /scratch/stefan/7787361/working/building/REAL300025581276 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581276 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581276/0 /scratch/stefan/7787361/working/building/REAL300025581276 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/787 `/scratch/stefan/7787361/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC2(CC(C(=O)NCCC3=NC(=O)O[N-]3)=NO2)C1) `REAL300025581276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581276 none CC(C)(C)OC(=O)N1CCCC2(CC(C(=O)NCCC3=NC(=O)O[N-]3)=NO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 150, 107, 150, 107, 107, 107, 107, 107, 107, 44, 44, 44, 20, 8, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 107, 107, 107, 107, 107, 107, 107, 44, 20, 21, 8, 8, 107, 107] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 497 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581276 none CC(C)(C)OC(=O)N1CCCC2(CC(C(=O)NCCC3=NC(=O)O[N-]3)=NO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 51, 57, 107, 107, 107, 107, 107, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 51, 51, 57, 57, 1, 1] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581276 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581276 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581276/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581276 Building REAL300025581277 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581277' /scratch/stefan/7787361/working/building/REAL300025581277 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581277 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581277/0 /scratch/stefan/7787361/working/building/REAL300025581277 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/788 `/scratch/stefan/7787361/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C(F)(F)F)=CC=C1Cl) `REAL300025581277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581277 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C(F)(F)F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 7, 7, 43, 71, 165, 165, 165, 165, 165, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 43, 43, 71, 71, 1, 1, 1] 165 rigid atoms, others: [1, 11, 12, 13, 14, 18, 19, 20, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 451 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581277 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C(F)(F)F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [91, 91, 23, 8, 1, 1, 1, 1, 1, 1, 1, 91, 165, 165, 165, 165, 165, 165, 124, 165, 165, 165, 91, 23, 23, 8, 8, 165, 139, 165] 165 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 501 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581277 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581277 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581277/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581277 Building REAL300025581278 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581278' /scratch/stefan/7787361/working/building/REAL300025581278 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581278 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581278/0 /scratch/stefan/7787361/working/building/REAL300025581278 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/789 `/scratch/stefan/7787361/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)C(Br)=CS1) `REAL300025581278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581278 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)C(Br)=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'Br', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 1, 17, 1, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [6, 1, 6, 6, 38, 64, 175, 175, 175, 175, 175, 1, 1, 1, 1, 1, 1, 1, 6, 38, 38, 64, 64, 1] 175 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 435 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581278 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)C(Br)=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'Br', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 1, 17, 1, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [77, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 77, 175, 175, 175, 175, 175, 175, 77, 25, 25, 8, 8, 175] 175 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581278 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581278 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581278/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581278 Building REAL300025581279 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581279' /scratch/stefan/7787361/working/building/REAL300025581279 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581279 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581279/0 /scratch/stefan/7787361/working/building/REAL300025581279 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/790 `/scratch/stefan/7787361/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCCCCCCC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581279 none CCCCCCCCCCCCC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 187, 171, 155, 139, 123, 107, 91, 69, 69, 61, 37, 61, 61, 37, 37, 15, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 187, 187, 171, 171, 155, 155, 139, 139, 123, 123, 107, 107, 91, 91, 69, 69, 69, 69, 61, 61, 61, 61, 61, 61, 37, 15, 15, 8, 8] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 911 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581279 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581279 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581279/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581279 Building REAL300025581280 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581280' /scratch/stefan/7787361/working/building/REAL300025581280 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581280 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581280/0 /scratch/stefan/7787361/working/building/REAL300025581280 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/791 `/scratch/stefan/7787361/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C(=O)NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21) `REAL300025581280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581280 none CCN1C(=O)NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 107, 107, 107, 107, 107, 107, 107, 41, 41, 41, 20, 8, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 201, 201, 201, 201, 201, 107, 107, 40, 20, 20, 8, 8, 107, 107] 201 rigid atoms, others: [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: 824 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581280 none CCN1C(=O)NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 45, 107, 107, 107, 107, 107, 1, 1, 1, 5, 5, 5, 4, 4, 1, 1, 5, 29, 29, 45, 45, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 20, 21, 22, 36, 28, 29] set([0, 32, 34, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581280 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581280 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581280/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581280 Building REAL300025581281 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581281' /scratch/stefan/7787361/working/building/REAL300025581281 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581281 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581281/0 /scratch/stefan/7787361/working/building/REAL300025581281 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/792 `/scratch/stefan/7787361/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2NC(=O)N(C3CC3)C2=C1) `REAL300025581281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581281 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2NC(=O)N(C3CC3)C2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 18, 18, 68, 78, 201, 201, 201, 201, 201, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 18, 68, 68, 78, 78, 6, 6, 6, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37]) total number of confs: 455 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581281 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2NC(=O)N(C3CC3)C2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 28, 36, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 5, 28, 28, 36, 36, 1, 1, 1, 6, 6, 6, 6, 6, 1] 201 rigid atoms, others: [1, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581281 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2NC(=O)N(C3CC3)C2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 19, 8, 1, 1, 1, 1, 1, 1, 1, 47, 121, 121, 121, 121, 121, 121, 121, 121, 201, 201, 121, 121, 47, 19, 19, 8, 8, 121, 121, 121, 201, 201, 201, 201, 201, 121] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 597 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581281 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581281 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581281/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581281 Building REAL300025581282 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581282' /scratch/stefan/7787361/working/building/REAL300025581282 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581282 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581282/0 /scratch/stefan/7787361/working/building/REAL300025581282 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/793 `/scratch/stefan/7787361/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCN(C(=O)OCC1=CC=CC=C1)C2) `REAL300025581282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581282 none O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCN(C(=O)OCC1=CC=CC=C1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 25, 61, 61, 137, 138, 201, 201, 201, 201, 201, 25, 25, 25, 25, 25, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 25, 61, 137, 137, 138, 138, 25, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 1, 25, 25] 201 rigid atoms, others: [42, 43, 44, 45, 46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 643 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581282 none O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCN(C(=O)OCC1=CC=CC=C1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 25, 26, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 25, 25, 13, 25, 25, 1, 7, 25, 25, 26, 26, 1, 1, 1, 1, 1, 1, 1, 12, 12, 25, 25, 13, 25, 25, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 38, 33, 47, 11, 12, 13, 14, 15, 16, 17, 48, 39, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581282 none O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCN(C(=O)OCC1=CC=CC=C1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 9, 6, 1, 1, 1, 1, 1, 1, 1, 22, 60, 60, 60, 60, 60, 60, 98, 98, 98, 201, 201, 201, 201, 201, 201, 60, 22, 9, 9, 6, 6, 60, 60, 60, 60, 60, 60, 60, 201, 201, 201, 201, 201, 201, 201, 60, 60] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 786 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581282 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581282 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581282/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581282 Building REAL300025581283 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581283' /scratch/stefan/7787361/working/building/REAL300025581283 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581283 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581283/0 /scratch/stefan/7787361/working/building/REAL300025581283 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/794 `/scratch/stefan/7787361/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581283 none CC(C)(C)OC(=O)N1CCCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 139, 200, 139, 139, 139, 139, 139, 52, 52, 52, 19, 8, 1, 1, 1, 1, 1, 1, 1, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 139, 139, 139, 139, 139, 139, 139, 52, 19, 19, 8, 8, 139, 139] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 668 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581283 none CC(C)(C)OC(=O)N1CCCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 49, 58, 139, 139, 139, 139, 139, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 49, 49, 58, 58, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 48, 40, 41, 24, 39, 49, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581283 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581283 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581283/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581283 Building REAL300025581284 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581284' /scratch/stefan/7787361/working/building/REAL300025581284 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581284 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581284/0 /scratch/stefan/7787361/working/building/REAL300025581284 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/795 `/scratch/stefan/7787361/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC[C@H](NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581284 none CC(C)OC[C@H](NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 138, 168, 94, 79, 35, 79, 79, 93, 114, 114, 114, 114, 114, 114, 35, 35, 14, 7, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 168, 168, 168, 94, 94, 93, 114, 114, 114, 114, 114, 114, 114, 114, 114, 35, 14, 14, 7, 7] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 805 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581284 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581284 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581284/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581284 Building REAL300025581285 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581285' /scratch/stefan/7787361/working/building/REAL300025581285 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581285 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581285/0 /scratch/stefan/7787361/working/building/REAL300025581285 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/796 `/scratch/stefan/7787361/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1Cl) `REAL300025581285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581285 none CC(C)(C)OC(=O)NC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 19, 13, 19, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 13, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6] 22 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581285 none CC(C)(C)OC(=O)NC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3] 22 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 25, 26, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581285 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581285 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581285/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581285 Building REAL300025581286 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581286' /scratch/stefan/7787361/working/building/REAL300025581286 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581286 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581286/0 /scratch/stefan/7787361/working/building/REAL300025581286 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/797 `/scratch/stefan/7787361/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1) `REAL300025581286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581286 none CC(C)(C)OC(=O)NCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 196, 158, 196, 130, 75, 29, 29, 29, 16, 16, 16, 8, 5, 1, 1, 1, 1, 1, 1, 1, 29, 29, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 130, 130, 75, 75, 29, 16, 8, 8, 5, 5] 201 rigid atoms, others: [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]) total number of confs: 822 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581286 none CC(C)(C)OC(=O)NCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 39, 29, 39, 20, 8, 1, 1, 1, 1, 1, 5, 5, 5, 12, 13, 29, 29, 29, 29, 29, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 29, 20, 20, 8, 8, 1, 5, 12, 12, 13, 13] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581286 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581286 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581286/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581286 Building REAL300025581287 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581287' /scratch/stefan/7787361/working/building/REAL300025581287 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581287 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581287/0 /scratch/stefan/7787361/working/building/REAL300025581287 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/798 `/scratch/stefan/7787361/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2=CC=CC=C2C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581287 none CC(C)(C)OC(=O)N1CC2=CC=CC=C2C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 153, 113, 153, 113, 113, 113, 113, 113, 113, 113, 113, 95, 54, 54, 55, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 113, 113, 113, 113, 113, 113, 95, 95, 54, 19, 19, 8, 8] 201 rigid atoms, others: [21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 699 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581287 none CC(C)(C)OC(=O)N1CC2=CC=CC=C2C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 8, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 45, 53, 113, 113, 113, 113, 113, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 45, 45, 53, 53] 201 rigid atoms, others: [43, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 39, 42, 5] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581287 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581287 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581287/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581287 Building REAL300025581288 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581288' /scratch/stefan/7787361/working/building/REAL300025581288 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581288 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581288/0 /scratch/stefan/7787361/working/building/REAL300025581288 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/799 `/scratch/stefan/7787361/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CO[C@H](C(=O)NCCC2=NC(=O)O[N-]2)[C@H]1C1=CC=CN=C1) `REAL300025581288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581288 none CN1C(=O)CO[C@H](C(=O)NCCC2=NC(=O)O[N-]2)[C@H]1C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 77, 93, 201, 201, 201, 201, 201, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 18, 77, 77, 93, 93, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 536 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581288 none CN1C(=O)CO[C@H](C(=O)NCCC2=NC(=O)O[N-]2)[C@H]1C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 133, 133, 133, 71, 133, 71, 71, 22, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 201, 201, 201, 201, 201, 133, 133, 133, 133, 133, 70, 23, 23, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [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, 39, 40]) total number of confs: 546 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581288 none CN1C(=O)CO[C@H](C(=O)NCCC2=NC(=O)O[N-]2)[C@H]1C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 43, 56, 133, 133, 133, 133, 133, 1, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 10, 43, 43, 56, 56, 3, 3, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581288 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581288 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581288/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581288 Building REAL300025581289 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581289' /scratch/stefan/7787361/working/building/REAL300025581289 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581289 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581289/0 /scratch/stefan/7787361/working/building/REAL300025581289 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/800 `/scratch/stefan/7787361/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1(C)C) `REAL300025581289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581289 none CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 164, 73, 164, 46, 46, 46, 18, 8, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 46, 19, 18, 8, 8, 73, 73, 73, 73, 73, 73, 73, 73] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44]) total number of confs: 605 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581289 none CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 5, 1, 5, 1, 1, 4, 4, 4, 18, 27, 73, 73, 73, 73, 73, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 18, 18, 27, 27, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [37, 38, 7, 8, 19, 20, 21, 22, 5] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581289 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581289 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581289/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581289 Building REAL300025581290 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581290' /scratch/stefan/7787361/working/building/REAL300025581290 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581290 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581290/0 /scratch/stefan/7787361/working/building/REAL300025581290 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/801 `/scratch/stefan/7787361/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)C1CCCC1) `REAL300025581290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581290 none CC(C)(C)OC(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 15, 3, 15, 1, 3, 13, 13, 13, 42, 42, 118, 118, 118, 118, 118, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 3, 13, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 39, 40, 41, 42, 7, 44, 45, 46, 47, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581290 none CC(C)(C)OC(=O)C(C(=O)NCCC1=NC(=O)O[N-]1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 193, 115, 192, 46, 46, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 115, 118, 118, 118, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 45, 9, 9, 8, 8, 118, 118, 118, 118, 118, 118, 118, 118, 118] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 693 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581290 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581290 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581290/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581290 Building REAL300025581291 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581291' /scratch/stefan/7787361/working/building/REAL300025581291 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581291 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581291/0 /scratch/stefan/7787361/working/building/REAL300025581291 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/802 `/scratch/stefan/7787361/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CNC1=O) `REAL300025581291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581291 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CNC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 63, 94, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 13, 63, 63, 94, 94, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 564 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581291 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CNC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 99, 201, 201, 201, 201, 201, 201, 201, 99, 24, 24, 8, 8, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581291 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581291 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581291/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581291 Building REAL300025581292 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581292' /scratch/stefan/7787361/working/building/REAL300025581292 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581292 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581292/0 /scratch/stefan/7787361/working/building/REAL300025581292 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/803 `/scratch/stefan/7787361/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(N2C=CN=C2)C=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581292 none O=C(CC1=CC=C(N2C=CN=C2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 81, 107, 107, 94, 107, 201, 201, 201, 201, 107, 107, 17, 8, 1, 1, 1, 1, 1, 1, 1, 81, 81, 107, 107, 201, 201, 201, 107, 107, 33, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 629 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581292 none O=C(CC1=CC=C(N2C=CN=C2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 5, 2, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 83, 87, 201, 201, 201, 201, 201, 10, 10, 6, 6, 1, 1, 1, 6, 6, 21, 83, 83, 87, 87] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 527 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581292 none O=C(CC1=CC=C(N2C=CN=C2)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 9, 9, 41, 45, 107, 107, 107, 107, 107, 4, 4, 1, 1, 6, 6, 6, 1, 1, 9, 41, 41, 45, 45] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 12, 13, 25, 26, 30, 31] set([0, 1, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581292 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581292 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581292/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581292 Building REAL300025581293 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581293' /scratch/stefan/7787361/working/building/REAL300025581293 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581293 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581293/0 /scratch/stefan/7787361/working/building/REAL300025581293 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/804 `/scratch/stefan/7787361/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CN2CCC2C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581293 none COC1=CC=C(CN2CCC2C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 169, 169, 201, 201, 169, 93, 93, 93, 93, 46, 46, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 169, 169, 93, 93, 93, 93, 93, 45, 8, 8, 8, 8, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 819 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581293 none COC1=CC=C(CN2CCC2C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 5, 23, 23, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26, 93, 93, 93, 93, 93, 23, 23, 23, 23, 23, 23, 23, 5, 5, 1, 1, 1, 1, 1, 7, 26, 26, 26, 26, 23, 23] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581293 none COC1=CC=C(CN2CCC2C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 57, 57, 57, 128, 128, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 8, 8, 23, 23, 23, 23, 23, 57, 128, 128, 128, 128, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 22, 23, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 616 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581293 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581293 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581293/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581293 Building REAL300025581294 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581294' /scratch/stefan/7787361/working/building/REAL300025581294 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581294 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581294/0 /scratch/stefan/7787361/working/building/REAL300025581294 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/805 `/scratch/stefan/7787361/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(N2CCOCC2)=NC=N1) `REAL300025581294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581294 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(N2CCOCC2)=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 27, 96, 117, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 28, 95, 95, 117, 117, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7] 201 rigid atoms, others: [32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37]) total number of confs: 599 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581294 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(N2CCOCC2)=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 51, 116, 116, 116, 117, 117, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 5, 28, 28, 51, 51, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1] 201 rigid atoms, others: [1, 37, 11, 12, 13, 14, 20, 21, 22, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 322 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581294 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(N2CCOCC2)=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 84, 117, 117, 117, 201, 201, 201, 201, 201, 117, 116, 116, 83, 24, 24, 8, 8, 117, 201, 201, 201, 201, 201, 201, 201, 201, 116] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 468 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581294 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581294 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581294/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581294 Building REAL300025581295 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581295' /scratch/stefan/7787361/working/building/REAL300025581295 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581295 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581295/0 /scratch/stefan/7787361/working/building/REAL300025581295 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/806 `/scratch/stefan/7787361/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C2=CC(O)=CC=C2C=C1) `REAL300025581295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581295 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C2=CC(O)=CC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 12, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 26, 29, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 26, 26, 29, 29, 2, 1, 2, 1, 1, 1, 1] 268 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 30]) total number of confs: 176 number of broken/clashed sets: 178 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581295 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C2=CC(O)=CC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 12, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 19, 8, 1, 1, 1, 1, 1, 1, 1, 40, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 40, 19, 19, 8, 8, 134, 67, 134, 67, 67, 67, 67] 268 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 459 number of broken/clashed sets: 178 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581295 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581295/1 /scratch/stefan/7787361/working/building/REAL300025581295 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/807 `/scratch/stefan/7787361/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C([O-])C2=CC(O)=CC=C2C=C1) `REAL300025581295.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581295 none O=C(NCCC1=NC(=O)O[N-]1)C1=C([O-])C2=CC(O)=CC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 12, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [8, 1, 8, 8, 16, 16, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 16, 16, 1, 2, 1, 1, 1, 1] 48 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 29]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581295 none O=C(NCCC1=NC(=O)O[N-]1)C1=C([O-])C2=CC(O)=CC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 12, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [21, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 21, 8, 8, 8, 8, 24, 48, 24, 24, 24, 24] 48 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581295 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581295 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581295/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581295/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581295 Building REAL300025581296 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581296' /scratch/stefan/7787361/working/building/REAL300025581296 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025581296 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581296/0 /scratch/stefan/7787361/working/building/REAL300025581296 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/808 `/scratch/stefan/7787361/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+](CCC1=CC=CC=C1)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581296 none C[N@H+](CCC1=CC=CC=C1)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 97, 121, 121, 161, 201, 201, 201, 201, 201, 201, 58, 58, 58, 17, 8, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 161, 161, 201, 201, 201, 201, 201, 201, 201, 97, 97, 58, 17, 17, 8, 8] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1006 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581296 none C[N@H+](CCC1=CC=CC=C1)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 45, 45, 45, 113, 116, 201, 201, 201, 201, 201, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 20, 20, 45, 113, 113, 116, 116] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 606 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581296 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581296/1 /scratch/stefan/7787361/working/building/REAL300025581296 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/809 `/scratch/stefan/7787361/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+](CCC1=CC=CC=C1)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581296.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581296 none C[N@@H+](CCC1=CC=CC=C1)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 98, 123, 123, 161, 201, 201, 201, 201, 201, 201, 59, 59, 59, 17, 8, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 161, 161, 201, 201, 201, 201, 201, 201, 201, 98, 98, 59, 17, 17, 8, 8] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1002 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581296 none C[N@@H+](CCC1=CC=CC=C1)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 44, 44, 44, 113, 116, 201, 201, 201, 201, 201, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 19, 19, 44, 113, 113, 116, 116] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 608 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581296 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `2' /scratch/stefan/7787361/working/building/REAL300025581296/2 /scratch/stefan/7787361/working/building/REAL300025581296 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 2 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/810 `/scratch/stefan/7787361/working/3D/810' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC1=CC=CC=C1)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581296.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025581296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581296/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581296 none CN(CCC1=CC=CC=C1)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 126, 157, 201, 201, 201, 201, 201, 201, 201, 48, 48, 48, 17, 7, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 126, 47, 18, 17, 7, 7] 201 rigid atoms, others: [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: 865 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581296 none CN(CCC1=CC=CC=C1)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 37, 37, 37, 116, 118, 201, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 37, 116, 116, 118, 118] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 25, 26, 27, 28, 29, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 589 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581296 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581296 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 2: /scratch/stefan/7787361/working/building/REAL300025581296/2.* 1: /scratch/stefan/7787361/working/building/REAL300025581296/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581296/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581296 Building REAL300025581297 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581297' /scratch/stefan/7787361/working/building/REAL300025581297 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581297 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581297/0 /scratch/stefan/7787361/working/building/REAL300025581297 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/811 `/scratch/stefan/7787361/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2N=CC=C(C3=CC=CN=C3)N2N=C1) `REAL300025581297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581297 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2N=CC=C(C3=CC=CN=C3)N2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 9, 20, 20, 72, 92, 201, 201, 201, 201, 201, 9, 9, 8, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 20, 72, 72, 92, 92, 9, 9, 1, 1, 1, 1, 9] 201 rigid atoms, others: [33, 34, 35, 36, 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, 37]) total number of confs: 537 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581297 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2N=CC=C(C3=CC=CN=C3)N2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 21, 31, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 4, 21, 21, 31, 31, 1, 1, 9, 9, 9, 9, 1] 201 rigid atoms, others: [32, 1, 37, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581297 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2N=CC=C(C3=CC=CN=C3)N2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 85, 24, 8, 1, 1, 1, 1, 1, 1, 1, 85, 117, 117, 117, 117, 117, 117, 201, 201, 201, 201, 201, 117, 117, 117, 85, 24, 24, 8, 8, 117, 117, 201, 201, 201, 201, 117] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 501 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581297 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581297 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581297/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581297 Building REAL300025581298 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581298' /scratch/stefan/7787361/working/building/REAL300025581298 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581298 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581298/0 /scratch/stefan/7787361/working/building/REAL300025581298 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/812 `/scratch/stefan/7787361/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=CC3=C2C=CC=C3)O1) `REAL300025581298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581298 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=CC3=C2C=CC=C3)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 65, 90, 152, 152, 152, 153, 153, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 64, 64, 90, 90, 1, 1, 1, 1, 1, 1, 1] 153 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581298 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=CC3=C2C=CC=C3)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 83, 153, 153, 152, 152, 152, 153, 153, 153, 153, 153, 152, 152, 82, 24, 24, 8, 8, 153, 153, 152, 153, 153, 153, 153] 153 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581298 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581298 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581298/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581298 Building REAL300025581299 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581299' /scratch/stefan/7787361/working/building/REAL300025581299 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581299 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581299/0 /scratch/stefan/7787361/working/building/REAL300025581299 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/813 `/scratch/stefan/7787361/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(C)(=O)=O)C=C(C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL300025581299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581299 none CC1=C(S(C)(=O)=O)C=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 5, 11, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 157, 157, 201, 201, 201, 157, 82, 82, 82, 20, 8, 1, 1, 1, 1, 1, 1, 1, 156, 157, 157, 157, 201, 201, 201, 157, 81, 20, 20, 8, 8] 201 rigid atoms, others: [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: 639 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581299 none CC1=C(S(C)(=O)=O)C=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 5, 11, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 12, 12, 12, 50, 61, 156, 156, 156, 156, 156, 1, 2, 2, 2, 5, 5, 5, 1, 12, 50, 50, 61, 61] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 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/7787361/working/building/REAL300025581299 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581299 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581299/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581299 Building REAL300025581300 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581300' /scratch/stefan/7787361/working/building/REAL300025581300 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581300 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581300/0 /scratch/stefan/7787361/working/building/REAL300025581300 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/814 `/scratch/stefan/7787361/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1C2CC3=C(Cl)C=CC=C3C21) `REAL300025581300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581300 none O=C(NCCC1=NC(=O)O[N-]1)C1C2CC3=C(Cl)C=CC=C3C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 76, 110, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 76, 76, 110, 110, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 601 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581300 none O=C(NCCC1=NC(=O)O[N-]1)C1C2CC3=C(Cl)C=CC=C3C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 24, 8, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581300 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581300 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581300/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581300 Building REAL300025581301 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581301' /scratch/stefan/7787361/working/building/REAL300025581301 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581301 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581301/0 /scratch/stefan/7787361/working/building/REAL300025581301 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/815 `/scratch/stefan/7787361/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC(Cl)=C1Cl) `REAL300025581301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581301 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 39, 39, 121, 124, 201, 201, 201, 201, 201, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 39, 121, 121, 124, 124, 6, 6, 1, 1, 1] 201 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 582 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581301 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 63, 67, 161, 161, 161, 161, 161, 1, 1, 1, 1, 1, 1, 6, 6, 4, 6, 6, 6, 6, 13, 63, 63, 67, 67, 1, 1, 6, 6, 6] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 395 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581301 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 9, 1, 1, 1, 1, 1, 1, 1, 51, 161, 161, 161, 161, 161, 201, 201, 201, 201, 201, 201, 201, 51, 19, 19, 9, 9, 161, 161, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 550 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581301 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581301 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581301/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581301 Building REAL300025581302 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581302' /scratch/stefan/7787361/working/building/REAL300025581302 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581302 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581302/0 /scratch/stefan/7787361/working/building/REAL300025581302 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/816 `/scratch/stefan/7787361/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2OC=C(CC(=O)NCCC3=NC(=O)O[N-]3)C2=C1) `REAL300025581302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581302 none CC1=CC=C2OC=C(CC(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 105, 35, 35, 35, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 105, 105, 35, 17, 17, 8, 8, 201] 201 rigid atoms, others: [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]) total number of confs: 541 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581302 none CC1=CC=C2OC=C(CC(=O)NCCC3=NC(=O)O[N-]3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 37, 37, 37, 99, 103, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 8, 8, 37, 99, 99, 103, 103, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 20, 21, 25, 26, 27] set([32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 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/7787361/working/building/REAL300025581302 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581302 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581302/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581302 Building REAL300025581303 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581303' /scratch/stefan/7787361/working/building/REAL300025581303 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581303 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581303/0 /scratch/stefan/7787361/working/building/REAL300025581303 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/817 `/scratch/stefan/7787361/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=C1) `REAL300025581303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581303 none CCCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 9, 1, 9, 32, 32, 32, 81, 81, 176, 176, 176, 176, 176, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 19, 19, 9, 32, 81, 81, 81, 81, 1, 1, 1, 1] 201 rigid atoms, others: [19, 3, 36, 37, 38, 15, 16, 17, 18, 35, 20, 21] set([0, 1, 2, 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: 526 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581303 none CCCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 138, 103, 39, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 104, 176, 176, 172, 176, 176, 176, 140, 140, 140, 140, 140, 138, 138, 104, 38, 8, 8, 8, 8, 176, 176, 176, 176] 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, 34, 35, 36, 37, 38]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581303 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581303 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581303/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581303 Building REAL300025581304 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581304' /scratch/stefan/7787361/working/building/REAL300025581304 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581304 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581304/0 /scratch/stefan/7787361/working/building/REAL300025581304 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/818 `/scratch/stefan/7787361/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1=NN(C)C=C1) `REAL300025581304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581304 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1=NN(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 39, 39, 39, 105, 115, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 39, 105, 105, 115, 115, 8, 8, 8, 2, 2, 2, 1, 1] 201 rigid atoms, others: [39, 40, 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: 591 number of broken/clashed sets: 101 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581304 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1=NN(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 61, 61, 20, 8, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 201, 201, 201, 201, 201, 120, 120, 120, 120, 60, 20, 20, 8, 8, 120, 120, 120, 201, 201, 201, 201, 201] 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, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 423 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581304 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1=NN(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 9, 33, 39, 119, 119, 119, 119, 119, 1, 1, 1, 1, 8, 8, 8, 8, 8, 2, 2, 2, 1, 9, 33, 33, 39, 39, 2, 2, 2, 8, 8, 8, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 282 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581304 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581304 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581304/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581304 Building REAL300025581305 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581305' /scratch/stefan/7787361/working/building/REAL300025581305 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581305 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581305/0 /scratch/stefan/7787361/working/building/REAL300025581305 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/819 `/scratch/stefan/7787361/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC(=O)C1=C(F)C=CC=C1F)NCCC1=NC(=O)O[N-]1) `REAL300025581305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581305 none O=C(CCC(=O)C1=C(F)C=CC=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 11, 1, 1, 15, 1, 1, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 109, 132, 183, 183, 201, 201, 201, 191, 201, 201, 201, 17, 7, 1, 1, 1, 1, 1, 1, 1, 109, 109, 132, 132, 201, 194, 201, 44, 17, 17, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 817 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581305 none O=C(CCC(=O)C1=C(F)C=CC=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 11, 1, 1, 15, 1, 1, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 32, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 101, 113, 201, 201, 201, 201, 201, 31, 31, 25, 25, 1, 1, 1, 58, 101, 101, 113, 113] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 634 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581305 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581305 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581305/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581305 Building REAL300025581306 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581306' /scratch/stefan/7787361/working/building/REAL300025581306 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581306 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581306/0 /scratch/stefan/7787361/working/building/REAL300025581306 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/820 `/scratch/stefan/7787361/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCC(C2=CC=CC=C2)NC1=O)NCCC1=NC(=O)O[N-]1) `REAL300025581306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581306 none O=C(CN1CCC(C2=CC=CC=C2)NC1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 194, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 194, 194, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 19, 19, 8, 8] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 733 number of broken/clashed sets: 23 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581306 none O=C(CN1CCC(C2=CC=CC=C2)NC1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 42, 42, 106, 112, 201, 201, 201, 201, 201, 11, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 42, 106, 106, 112, 112] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42]) total number of confs: 578 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581306 none O=C(CN1CCC(C2=CC=CC=C2)NC1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 1, 36, 36, 96, 104, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 36, 96, 96, 104, 104] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 13, 14, 15, 37, 27, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 563 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581306 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581306 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581306/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581306 Building REAL300025581307 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581307' /scratch/stefan/7787361/working/building/REAL300025581307 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581307 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581307/0 /scratch/stefan/7787361/working/building/REAL300025581307 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/821 `/scratch/stefan/7787361/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1CCO[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581307 none CC(C)(C)OC(=O)NC[C@@H]1CCO[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 13, 14, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 11, 11, 9, 9, 9, 9, 9, 7, 7, 7, 7] 14 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581307 none CC(C)(C)OC(=O)NC[C@@H]1CCO[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 7, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 3, 3, 1, 1, 1, 1, 2, 4, 4, 4, 4] 14 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581307 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581307 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581307/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581307 Building REAL300025581308 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581308' /scratch/stefan/7787361/working/building/REAL300025581308 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581308 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581308/0 /scratch/stefan/7787361/working/building/REAL300025581308 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/822 `/scratch/stefan/7787361/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)NC2CCCCC21) `REAL300025581308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581308 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)NC2CCCCC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 7, 7, 31, 48, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 31, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 113 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 304 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581308 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)NC2CCCCC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [64, 64, 21, 8, 1, 1, 1, 1, 1, 1, 1, 64, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 63, 21, 21, 8, 8, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113] 113 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 368 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581308 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581308 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581308/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581308 Building REAL300025581309 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581309' /scratch/stefan/7787361/working/building/REAL300025581309 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581309 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581309/0 /scratch/stefan/7787361/working/building/REAL300025581309 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/823 `/scratch/stefan/7787361/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CSN=N2)C=C1) `REAL300025581309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581309 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CSN=N2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 14, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 25, 25, 98, 129, 201, 201, 201, 201, 201, 1, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 25, 98, 98, 129, 129, 12, 12, 1, 12, 12] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 666 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581309 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CSN=N2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 14, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 16, 30, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 3, 16, 16, 30, 30, 1, 1, 12, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 20, 21, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581309 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CSN=N2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 14, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 81, 130, 130, 81, 130, 201, 201, 201, 201, 130, 130, 80, 25, 25, 8, 8, 130, 130, 201, 130, 130] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581309 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581309 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581309/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581309 Building REAL300025581310 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581310' /scratch/stefan/7787361/working/building/REAL300025581310 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581310 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581310/0 /scratch/stefan/7787361/working/building/REAL300025581310 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/824 `/scratch/stefan/7787361/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(Br)=C1) `REAL300025581310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581310 none CCSC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 108, 87, 129, 129, 87, 28, 28, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 201, 201, 201, 201, 201, 129, 129, 87, 87, 28, 8, 8, 8, 8, 129] 201 rigid atoms, others: [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]) total number of confs: 696 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581310 none CCSC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 6, 33, 33, 33, 71, 71, 129, 129, 129, 129, 129, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 6, 6, 33, 71, 71, 71, 71, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 19, 20, 21, 36, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581310 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581310 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581310/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581310 Building REAL300025581311 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581311' /scratch/stefan/7787361/working/building/REAL300025581311 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581311 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581311/0 /scratch/stefan/7787361/working/building/REAL300025581311 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/825 `/scratch/stefan/7787361/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CC=CC=C2CC1) `REAL300025581311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581311 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CC=CC=C2CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 67, 101, 197, 197, 197, 197, 197, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 67, 67, 101, 101, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 197 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 579 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581311 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CC=CC=C2CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 24, 8, 1, 1, 1, 1, 1, 1, 1, 105, 197, 197, 197, 197, 197, 197, 197, 197, 197, 197, 105, 25, 25, 8, 8, 197, 197, 197, 197, 197, 197, 197, 197, 197, 197, 197, 197, 197] 197 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 609 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581311 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581311 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581311/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581311 Building REAL300025581312 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581312' /scratch/stefan/7787361/working/building/REAL300025581312 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581312 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581312/0 /scratch/stefan/7787361/working/building/REAL300025581312 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/826 `/scratch/stefan/7787361/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(COC(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581312 none CC1=CC=C(COC(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 186, 114, 95, 40, 95, 40, 40, 16, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 186, 186, 95, 95, 95, 95, 40, 16, 16, 7, 7, 201, 201] 201 rigid atoms, others: [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: 811 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581312 none CC1=CC=C(COC(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 15, 27, 27, 39, 39, 39, 118, 124, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 5, 5, 27, 27, 27, 27, 39, 118, 118, 124, 124, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 651 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581312 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581312 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581312/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581312 Building REAL300025581313 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581313' /scratch/stefan/7787361/working/building/REAL300025581313 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581313 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581313/0 /scratch/stefan/7787361/working/building/REAL300025581313 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/827 `/scratch/stefan/7787361/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(Br)=CC=C2S1) `REAL300025581313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581313 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(Br)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 12, 65, 91, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 64, 64, 91, 91, 1, 1, 1, 1] 151 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 469 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581313 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(Br)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 80, 150, 150, 150, 150, 150, 150, 150, 150, 151, 80, 24, 24, 8, 8, 150, 150, 150, 150] 151 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581313 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581313 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581313/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581313 Building REAL300025581314 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581314' /scratch/stefan/7787361/working/building/REAL300025581314 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581314 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581314/0 /scratch/stefan/7787361/working/building/REAL300025581314 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/828 `/scratch/stefan/7787361/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2=C(C=CC=C2C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581314 none CC(C)(C)OC(=O)N1CCC2=C(C=CC=C2C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 121, 74, 121, 74, 74, 74, 74, 74, 74, 74, 74, 35, 35, 35, 17, 8, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 201, 201, 201, 201, 201, 201, 201, 74, 74, 74, 74, 74, 74, 74, 35, 17, 17, 8, 8, 74, 74] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 506 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581314 none CC(C)(C)OC(=O)N1CCC2=C(C=CC=C2C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 33, 37, 74, 74, 74, 74, 74, 1, 9, 9, 9, 8, 8, 8, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 8, 33, 33, 37, 37, 1, 1] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 14, 15, 16, 40, 50, 43, 41, 49, 27, 42, 5] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581314 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581314 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581314/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581314 Building REAL300025581315 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581315' /scratch/stefan/7787361/working/building/REAL300025581315 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581315 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581315/0 /scratch/stefan/7787361/working/building/REAL300025581315 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/829 `/scratch/stefan/7787361/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1(CC(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025581315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581315 none CC(C)(C)OC(=O)NC1(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 162, 120, 162, 120, 111, 50, 50, 50, 17, 8, 1, 1, 1, 1, 1, 1, 1, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 111, 111, 50, 17, 17, 8, 8, 120, 120, 120, 120] 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, 41, 42, 43]) total number of confs: 697 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581315 none CC(C)(C)OC(=O)NC1(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 5, 6, 6, 3, 2, 3, 1, 1, 1, 4, 21, 21, 21, 52, 53, 120, 120, 120, 120, 120, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 4, 4, 21, 52, 52, 53, 53, 1, 1, 1, 1] 201 rigid atoms, others: [7, 8, 9, 42, 43, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 39]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581315 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581315 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581315/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581315 Building REAL300025581316 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581316' /scratch/stefan/7787361/working/building/REAL300025581316 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581316 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581316/0 /scratch/stefan/7787361/working/building/REAL300025581316 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/830 `/scratch/stefan/7787361/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H](CC(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581316 none CC(C)(C)OC(=O)N1CCC[C@@H](CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 169, 149, 169, 149, 149, 149, 148, 108, 149, 36, 36, 36, 9, 9, 1, 1, 1, 1, 1, 1, 1, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 149, 149, 149, 149, 114, 114, 36, 9, 9, 9, 9, 149, 149] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 678 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581316 none CC(C)(C)OC(=O)N1CCC[C@@H](CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 28, 28, 28, 72, 72, 149, 149, 149, 149, 149, 1, 6, 6, 6, 5, 5, 5, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 28, 72, 72, 72, 72, 1, 1] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 48, 40, 25, 49, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581316 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581316 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581316/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581316 Building REAL300025581317 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581317' /scratch/stefan/7787361/working/building/REAL300025581317 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581317 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581317/0 /scratch/stefan/7787361/working/building/REAL300025581317 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/831 `/scratch/stefan/7787361/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=NN(C(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581317 none CC(C)(C)OC(=O)NC1=NN(C(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 11, 19, 11, 11, 11, 10, 8, 10, 10, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 10, 10, 10, 10, 10, 10, 8, 5, 5, 3, 3, 11, 11] 19 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581317 none CC(C)(C)OC(=O)NC1=NN(C(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 9, 9, 11, 11, 11, 11, 11, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 5, 9, 9, 9, 9, 1, 1] 19 rigid atoms, others: [7, 8, 9, 10, 11, 48, 49, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581317 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581317 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581317/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581317 Building REAL300025581318 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581318' /scratch/stefan/7787361/working/building/REAL300025581318 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581318 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581318/0 /scratch/stefan/7787361/working/building/REAL300025581318 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/832 `/scratch/stefan/7787361/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(OC1=CC=C(C(F)(F)F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581318 none CC(C)(OC1=CC=C(C(F)(F)F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 35, 104, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 35, 35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 107, 105, 107, 107, 107, 104, 201, 201, 201, 201, 34, 8, 8, 8, 8] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 544 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581318 none CC(C)(OC1=CC=C(C(F)(F)F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 15, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 15, 49, 49, 49, 98, 98, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 49, 98, 98, 98, 98] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 12, 13, 31] set([0, 1, 2, 9, 10, 11, 14, 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: 556 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581318 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581318 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581318/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581318 Building REAL300025581319 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581319' /scratch/stefan/7787361/working/building/REAL300025581319 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581319 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581319/0 /scratch/stefan/7787361/working/building/REAL300025581319 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/833 `/scratch/stefan/7787361/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(C1=CC=CC=C1)C1=CC=C(Cl)C=C1) `REAL300025581319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581319 none O=C(NCCC1=NC(=O)O[N-]1)C(C1=CC=CC=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 14, 14, 61, 90, 201, 201, 201, 201, 201, 1, 4, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 14, 61, 61, 90, 90, 4, 5, 5, 5, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 11, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 557 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581319 none O=C(NCCC1=NC(=O)O[N-]1)C(C1=CC=CC=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 14, 14, 61, 89, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 14, 61, 61, 89, 89, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39]) total number of confs: 547 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581319 none O=C(NCCC1=NC(=O)O[N-]1)C(C1=CC=CC=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 70, 22, 8, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 22, 22, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 760 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581319 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581319 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581319/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581319 Building REAL300025581320 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581320' /scratch/stefan/7787361/working/building/REAL300025581320 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581320 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581320/0 /scratch/stefan/7787361/working/building/REAL300025581320 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/834 `/scratch/stefan/7787361/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CSC(Br)=C1) `REAL300025581320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581320 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CSC(Br)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 14, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 9, 41, 41, 125, 127, 201, 201, 201, 201, 201, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 41, 125, 125, 127, 127, 9, 9, 1, 1] 201 rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 577 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581320 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CSC(Br)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 14, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 59, 61, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 12, 59, 59, 61, 61, 1, 1, 9, 9] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581320 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CSC(Br)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 14, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 16, 9, 1, 1, 1, 1, 1, 1, 1, 45, 138, 138, 138, 138, 138, 201, 201, 201, 201, 201, 45, 16, 16, 9, 9, 138, 138, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 531 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581320 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581320 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581320/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581320 Building REAL300025581321 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581321' /scratch/stefan/7787361/working/building/REAL300025581321 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581321 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581321/0 /scratch/stefan/7787361/working/building/REAL300025581321 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/835 `/scratch/stefan/7787361/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2CC2(F)F)C=C1) `REAL300025581321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581321 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2CC2(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 8, 64, 64, 129, 129, 201, 201, 201, 201, 201, 8, 39, 39, 8, 1, 1, 1, 1, 1, 1, 39, 39, 64, 129, 129, 129, 129, 39, 39, 1, 1, 1, 39, 39] 201 rigid atoms, others: [32, 15, 16, 17, 18, 19, 20, 30, 31] 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, 33, 34]) total number of confs: 666 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581321 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2CC2(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 14, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 13, 39, 39, 39, 39, 1, 1, 3, 13, 13, 14, 14, 1, 1, 39, 39, 39, 1, 1] 201 rigid atoms, others: [1, 34, 33, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 191 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581321 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2CC2(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 15, 7, 1, 1, 1, 1, 1, 1, 1, 35, 56, 56, 35, 56, 159, 201, 201, 201, 201, 56, 56, 35, 15, 15, 7, 7, 56, 56, 201, 201, 201, 56, 56] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 577 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581321 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581321 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581321/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581321 Building REAL300025581322 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581322' /scratch/stefan/7787361/working/building/REAL300025581322 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581322 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581322/0 /scratch/stefan/7787361/working/building/REAL300025581322 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/836 `/scratch/stefan/7787361/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC(F)(F)F)C(Cl)=C1) `REAL300025581322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581322 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC(F)(F)F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 27, 31, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 7, 19, 19, 19, 1, 1, 1, 5, 27, 27, 31, 31, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 20, 21, 22, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581322 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC(F)(F)F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 17, 8, 1, 1, 1, 1, 1, 1, 1, 48, 131, 131, 131, 131, 201, 201, 201, 201, 131, 131, 131, 48, 17, 17, 8, 8, 131, 131, 131] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 426 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581322 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581322 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581322/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581322 Building REAL300025581323 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581323' /scratch/stefan/7787361/working/building/REAL300025581323 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581323 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581323/0 /scratch/stefan/7787361/working/building/REAL300025581323 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/837 `/scratch/stefan/7787361/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Br) `REAL300025581323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581323 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 186, 186, 79, 79, 79, 23, 8, 1, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 201, 201, 201, 186, 78, 24, 24, 8, 8, 186, 186] 201 rigid atoms, others: [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]) total number of confs: 441 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581323 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 29, 53, 186, 186, 186, 186, 186, 1, 1, 1, 1, 4, 4, 4, 1, 5, 29, 29, 53, 53, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 23, 29, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581323 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581323 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581323/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581323 Building REAL300025581324 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581324' /scratch/stefan/7787361/working/building/REAL300025581324 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581324 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581324/0 /scratch/stefan/7787361/working/building/REAL300025581324 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/838 `/scratch/stefan/7787361/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC(F)(F)F) `REAL300025581324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581324 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 43, 43, 43, 17, 8, 1, 1, 1, 1, 1, 1, 1, 114, 114, 74, 114, 201, 201, 201, 201, 114, 114, 114, 114, 43, 17, 17, 8, 8, 114, 114] 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: 624 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581324 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 27, 30, 114, 114, 114, 114, 114, 1, 1, 1, 1, 7, 20, 19, 20, 2, 2, 2, 1, 5, 27, 27, 30, 30, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 15, 16, 17, 18, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581324 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581324 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581324/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581324 Building REAL300025581325 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581325' /scratch/stefan/7787361/working/building/REAL300025581325 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581325 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581325/0 /scratch/stefan/7787361/working/building/REAL300025581325 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/839 `/scratch/stefan/7787361/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1COC2=CC(F)=CC=C2C1) `REAL300025581325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581325 none O=C(NCCC1=NC(=O)O[N-]1)C1COC2=CC(F)=CC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 1, 13, 13, 75, 104, 166, 166, 166, 166, 166, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 75, 75, 104, 104, 1, 1, 1, 1, 1, 1, 1, 1] 166 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 527 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581325 none O=C(NCCC1=NC(=O)O[N-]1)C1COC2=CC(F)=CC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [86, 86, 24, 8, 1, 1, 1, 1, 1, 1, 1, 86, 166, 166, 166, 166, 166, 166, 166, 166, 166, 166, 86, 24, 24, 8, 8, 166, 166, 166, 166, 166, 166, 166, 166] 166 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 523 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581325 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581325 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581325/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581325 Building REAL300025581326 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581326' /scratch/stefan/7787361/working/building/REAL300025581326 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581326 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581326/0 /scratch/stefan/7787361/working/building/REAL300025581326 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/840 `/scratch/stefan/7787361/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(S(C)(=O)=O)O1) `REAL300025581326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581326 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(S(C)(=O)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 5, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 60, 60, 60, 19, 8, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 201, 201, 201, 148, 148, 148, 148, 60, 19, 19, 8, 8, 148, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 648 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581326 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(S(C)(=O)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 5, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 45, 50, 148, 148, 148, 148, 148, 1, 1, 1, 6, 6, 6, 1, 2, 2, 2, 9, 45, 45, 50, 50, 1, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 20, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581326 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581326 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581326/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581326 Building REAL300025581327 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581327' /scratch/stefan/7787361/working/building/REAL300025581327 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581327 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581327/0 /scratch/stefan/7787361/working/building/REAL300025581327 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/841 `/scratch/stefan/7787361/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CN2C(=O)C3=CC=CC=C3C2=O)C=C(C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL300025581327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581327 none CC1=C(CN2C(=O)C3=CC=CC=C3C2=O)C=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 49, 49, 49, 18, 7, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 201, 201, 201, 201, 201, 201, 84, 49, 19, 19, 7, 7] 201 rigid atoms, others: [21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 707 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581327 none CC1=C(CN2C(=O)C3=CC=CC=C3C2=O)C=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 30, 30, 30, 87, 115, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 10, 30, 87, 87, 115, 115] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 36, 37] set([0, 1, 2, 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]) total number of confs: 620 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581327 none CC1=C(CN2C(=O)C3=CC=CC=C3C2=O)C=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 6, 6, 7, 28, 36, 84, 84, 84, 84, 84, 1, 2, 2, 2, 6, 6, 8, 8, 8, 8, 1, 7, 28, 28, 36, 36] 201 rigid atoms, others: [0, 1, 2, 3, 38, 15, 16, 17, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581327 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581327 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581327/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581327 Building REAL300025581328 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581328' /scratch/stefan/7787361/working/building/REAL300025581328 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581328 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581328/0 /scratch/stefan/7787361/working/building/REAL300025581328 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/842 `/scratch/stefan/7787361/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1COC(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581328 none CC1=CC=CC=C1COC(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 201, 201, 143, 96, 73, 40, 73, 40, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 143, 201, 201, 143, 143, 73, 73, 73, 73, 39, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 799 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581328 none CC1=CC=CC=C1COC(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 40, 40, 57, 57, 57, 114, 114, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 7, 7, 40, 40, 40, 40, 57, 114, 114, 114, 114] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581328 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581328 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581328/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581328 Building REAL300025581329 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581329' /scratch/stefan/7787361/working/building/REAL300025581329 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581329 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581329/0 /scratch/stefan/7787361/working/building/REAL300025581329 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/843 `/scratch/stefan/7787361/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C(F)(F)F)=C1) `REAL300025581329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581329 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 37, 59, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 37, 37, 59, 59, 1, 1] 142 rigid atoms, others: [1, 11, 12, 13, 14, 15, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 20, 21, 22, 23, 24]) total number of confs: 379 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581329 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 22, 8, 1, 1, 1, 1, 1, 1, 1, 59, 142, 142, 142, 142, 142, 142, 142, 142, 58, 22, 22, 8, 8, 142, 142] 142 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581329 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581329 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581329/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581329 Building REAL300025581330 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581330' /scratch/stefan/7787361/working/building/REAL300025581330 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581330 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581330/0 /scratch/stefan/7787361/working/building/REAL300025581330 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/844 `/scratch/stefan/7787361/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CC[C@@H](C2=CC=CC=C2)C1) `REAL300025581330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581330 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CC[C@@H](C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 3, 19, 19, 82, 104, 201, 201, 201, 201, 201, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 19, 82, 82, 104, 104, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3] 201 rigid atoms, others: [33, 34, 35, 36, 37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 565 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581330 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CC[C@@H](C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 52, 73, 183, 183, 183, 183, 183, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 11, 52, 52, 73, 73, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1] 201 rigid atoms, others: [32, 1, 38, 39, 11, 12, 13, 14, 15, 16, 17, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 457 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581330 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CC[C@@H](C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 23, 8, 1, 1, 1, 1, 1, 1, 1, 74, 183, 183, 183, 183, 183, 183, 201, 201, 183, 201, 201, 183, 74, 23, 23, 8, 8, 183, 183, 183, 183, 201, 201, 183, 201, 201, 183, 183] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 642 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581330 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581330 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581330/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581330 Building REAL300025581331 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581331' /scratch/stefan/7787361/working/building/REAL300025581331 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581331 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581331/0 /scratch/stefan/7787361/working/building/REAL300025581331 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/845 `/scratch/stefan/7787361/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C1CCOCC1) `REAL300025581331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581331 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 5, 23, 23, 23, 72, 104, 193, 193, 193, 193, 193, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 23, 72, 72, 104, 104, 1, 1, 1, 1, 1, 1, 1, 1, 1] 193 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 598 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581331 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [165, 165, 165, 99, 99, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 193, 193, 193, 193, 193, 165, 165, 165, 165, 98, 24, 24, 8, 8, 193, 193, 193, 193, 193, 193, 193, 193, 193] 193 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, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 511 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581331 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 9, 9, 34, 60, 165, 165, 165, 165, 165, 1, 1, 1, 5, 5, 5, 5, 5, 2, 2, 2, 1, 9, 34, 34, 60, 60, 5, 5, 5, 5, 5, 5, 5, 5, 5] 193 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 424 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581331 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581331 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581331/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581331 Building REAL300025581332 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581332' /scratch/stefan/7787361/working/building/REAL300025581332 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581332 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581332/0 /scratch/stefan/7787361/working/building/REAL300025581332 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/846 `/scratch/stefan/7787361/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(N2CC(C(=O)NCCC3=NC(=O)O[N-]3)CC2=O)C=N1) `REAL300025581332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581332 none CN1C=C(N2CC(C(=O)NCCC3=NC(=O)O[N-]3)CC2=O)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 148, 148, 148, 59, 59, 59, 19, 8, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 201, 201, 201, 201, 201, 201, 148, 148, 148, 58, 19, 19, 8, 8, 148, 148, 201] 201 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, 37]) total number of confs: 544 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581332 none CN1C=C(N2CC(C(=O)NCCC3=NC(=O)O[N-]3)CC2=O)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 47, 58, 148, 148, 148, 148, 148, 1, 1, 1, 3, 3, 4, 4, 4, 4, 1, 1, 1, 9, 47, 47, 58, 58, 1, 1, 4] 201 rigid atoms, others: [35, 3, 4, 5, 6, 7, 18, 19, 20, 36, 27, 28, 29] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 37]) total number of confs: 373 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581332 none CN1C=C(N2CC(C(=O)NCCC3=NC(=O)O[N-]3)CC2=O)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 20, 20, 20, 82, 94, 201, 201, 201, 201, 201, 3, 3, 4, 1, 1, 2, 2, 2, 1, 3, 3, 3, 20, 82, 82, 94, 94, 3, 3, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 532 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581332 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581332 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581332/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581332 Building REAL300025581333 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581333' /scratch/stefan/7787361/working/building/REAL300025581333 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581333 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581333/0 /scratch/stefan/7787361/working/building/REAL300025581333 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/847 `/scratch/stefan/7787361/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](OC1=CC=C(Cl)C=C1Cl)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581333 none C[C@H](OC1=CC=C(Cl)C=C1Cl)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 117, 111, 177, 201, 201, 198, 201, 201, 201, 201, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 117, 117, 111, 201, 201, 201, 38, 9, 9, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 614 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581333 none C[C@H](OC1=CC=C(Cl)C=C1Cl)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 54, 54, 54, 111, 111, 201, 201, 201, 201, 201, 16, 16, 16, 1, 1, 1, 54, 111, 111, 111, 111] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 583 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581333 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581333 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581333/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581333 Building REAL300025581334 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581334' /scratch/stefan/7787361/working/building/REAL300025581334 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581334 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581334/0 /scratch/stefan/7787361/working/building/REAL300025581334 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/848 `/scratch/stefan/7787361/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CCC(=O)NCCC2=NC(=O)O[N-]2)C(Br)=C1) `REAL300025581334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581334 none COC1=CC=C(CCC(=O)NCCC2=NC(=O)O[N-]2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 196, 196, 196, 143, 117, 33, 33, 33, 15, 7, 1, 1, 1, 1, 1, 1, 1, 196, 196, 196, 201, 201, 201, 196, 196, 143, 143, 117, 117, 33, 15, 15, 7, 7, 196] 201 rigid atoms, others: [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]) total number of confs: 695 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581334 none COC1=CC=C(CCC(=O)NCCC2=NC(=O)O[N-]2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 3, 5, 25, 25, 25, 71, 71, 196, 196, 196, 196, 196, 1, 1, 1, 3, 3, 3, 1, 1, 3, 3, 5, 5, 25, 71, 71, 71, 71, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 25, 26, 36] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 463 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581334 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581334 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581334/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581334 Building REAL300025581335 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581335' /scratch/stefan/7787361/working/building/REAL300025581335 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581335 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581335/0 /scratch/stefan/7787361/working/building/REAL300025581335 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/849 `/scratch/stefan/7787361/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(CN2C=CN=N2)=C1) `REAL300025581335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581335 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(CN2C=CN=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 19, 45, 45, 119, 123, 201, 201, 201, 201, 201, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 19, 45, 119, 119, 123, 123, 19, 19, 19, 8, 8, 1, 1, 19] 201 rigid atoms, others: [33, 34, 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, 35]) total number of confs: 600 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581335 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(CN2C=CN=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 23, 27, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 1, 5, 23, 23, 27, 27, 1, 1, 1, 6, 6, 19, 19, 1] 201 rigid atoms, others: [1, 35, 11, 12, 13, 14, 15, 16, 22, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581335 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(CN2C=CN=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 15, 7, 1, 1, 1, 1, 1, 1, 1, 35, 76, 76, 50, 76, 76, 179, 201, 201, 201, 201, 76, 35, 15, 15, 7, 7, 76, 76, 76, 179, 179, 201, 201, 76] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 826 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581335 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581335 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581335/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581335 Building REAL300025581336 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581336' /scratch/stefan/7787361/working/building/REAL300025581336 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581336 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581336/0 /scratch/stefan/7787361/working/building/REAL300025581336 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/850 `/scratch/stefan/7787361/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(C(F)(F)F)=CC=C2S1) `REAL300025581336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581336 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(C(F)(F)F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 67, 91, 157, 157, 157, 157, 157, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 12, 66, 66, 91, 91, 1, 1, 1, 1] 157 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581336 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(C(F)(F)F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 24, 8, 1, 1, 1, 1, 1, 1, 1, 84, 156, 156, 156, 156, 156, 157, 157, 157, 156, 156, 156, 156, 84, 24, 24, 8, 8, 156, 156, 156, 156] 157 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581336 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581336 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581336/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581336 Building REAL300025581337 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581337' /scratch/stefan/7787361/working/building/REAL300025581337 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581337 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581337/0 /scratch/stefan/7787361/working/building/REAL300025581337 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/851 `/scratch/stefan/7787361/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(OCC2=CC=CC=C2)C(F)=C1) `REAL300025581337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581337 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(OCC2=CC=CC=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 49, 49, 134, 134, 201, 201, 201, 201, 201, 24, 26, 26, 27, 13, 3, 1, 1, 1, 1, 1, 1, 1, 26, 27, 26, 49, 134, 134, 134, 134, 27, 3, 3, 1, 1, 1, 1, 1, 27] 201 rigid atoms, others: [35, 36, 37, 38, 39, 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, 40]) total number of confs: 681 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581337 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(OCC2=CC=CC=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 12, 14, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 2, 10, 26, 26, 16, 26, 26, 1, 1, 1, 3, 12, 12, 14, 14, 1, 10, 10, 27, 27, 26, 27, 27, 1] 201 rigid atoms, others: [32, 1, 40, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581337 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C(OCC2=CC=CC=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 13, 7, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 75, 201, 201, 201, 201, 201, 201, 50, 50, 50, 28, 13, 13, 7, 7, 50, 201, 201, 201, 201, 201, 201, 201, 50] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581337 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581337 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581337/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581337 Building REAL300025581338 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581338' /scratch/stefan/7787361/working/building/REAL300025581338 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581338 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581338/0 /scratch/stefan/7787361/working/building/REAL300025581338 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/852 `/scratch/stefan/7787361/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)N=C2COCCN21) `REAL300025581338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581338 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)N=C2COCCN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 8, 1, 5, 12, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 37, 61, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 61, 61, 1, 1, 1, 1, 1, 1] 148 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 395 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581338 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)N=C2COCCN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 8, 1, 5, 12, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 20, 8, 1, 1, 1, 1, 1, 1, 1, 95, 148, 148, 148, 148, 148, 148, 148, 148, 148, 95, 20, 20, 8, 8, 148, 148, 148, 148, 148, 148] 148 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 364 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581338 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581338 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581338/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581338 Building REAL300025581339 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581339' /scratch/stefan/7787361/working/building/REAL300025581339 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581339 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581339/0 /scratch/stefan/7787361/working/building/REAL300025581339 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/853 `/scratch/stefan/7787361/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)N(C2=CC=C(F)C(F)=C2)C1) `REAL300025581339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581339 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)N(C2=CC=C(F)C(F)=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 5, 32, 32, 108, 109, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 32, 108, 108, 109, 109, 5, 5, 5, 1, 1, 1, 5, 5] 201 rigid atoms, others: [33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 567 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581339 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)N(C2=CC=C(F)C(F)=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 37, 38, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 9, 37, 37, 38, 38, 1, 1, 1, 5, 5, 5, 1, 1] 201 rigid atoms, others: [32, 1, 36, 37, 11, 12, 13, 14, 15, 16, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581339 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)N(C2=CC=C(F)C(F)=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 16, 8, 1, 1, 1, 1, 1, 1, 1, 37, 85, 85, 85, 85, 85, 201, 201, 201, 201, 201, 201, 201, 85, 37, 16, 16, 8, 8, 85, 85, 85, 201, 201, 201, 85, 85] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581339 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581339 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581339/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581339 Building REAL300025581340 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581340' /scratch/stefan/7787361/working/building/REAL300025581340 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581340 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581340/0 /scratch/stefan/7787361/working/building/REAL300025581340 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/854 `/scratch/stefan/7787361/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1[C@H]2CC[C@]3(COC(=O)[C@H]13)O2) `REAL300025581340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581340 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1[C@H]2CC[C@]3(COC(=O)[C@H]13)O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 7, 5, 5, 5, 5, 12, 1, 11, 5, 7, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 3, 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: [7, 1, 7, 7, 27, 44, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 27, 44, 44, 1, 1, 1, 1, 1, 1] 96 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581340 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1[C@H]2CC[C@]3(COC(=O)[C@H]13)O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 7, 5, 5, 5, 5, 12, 1, 11, 5, 7, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 3, 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: [79, 79, 23, 8, 1, 1, 1, 1, 1, 1, 1, 79, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 79, 23, 23, 8, 8, 96, 96, 96, 96, 96, 96] 96 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581340 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581340 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581340/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581340 Building REAL300025581341 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581341' /scratch/stefan/7787361/working/building/REAL300025581341 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581341 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581341/0 /scratch/stefan/7787361/working/building/REAL300025581341 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/855 `/scratch/stefan/7787361/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)[N-]C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025581341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581341 none CS(=O)(=O)[N-]C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 201, 201, 114, 114, 114, 114, 57, 58, 58, 23, 8, 1, 1, 1, 1, 1, 1, 1, 114, 114, 201, 201, 201, 114, 114, 57, 24, 24, 8, 8, 114] 201 rigid atoms, others: [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: 503 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581341 none CS(=O)(=O)[N-]C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 18, 18, 1, 1, 1, 1, 1, 1, 5, 5, 5, 27, 42, 114, 114, 114, 114, 114, 1, 1, 18, 18, 18, 1, 1, 5, 27, 27, 42, 42, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581341 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581341/1 /scratch/stefan/7787361/working/building/REAL300025581341 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/856 `/scratch/stefan/7787361/working/3D/856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025581341.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581341 none CS(=O)(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 201, 201, 133, 133, 133, 133, 60, 60, 60, 17, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 201, 201, 201, 182, 133, 133, 60, 17, 17, 8, 8, 133] 201 rigid atoms, others: [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: 585 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581341 none CS(=O)(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 38, 133, 133, 133, 133, 133, 1, 1, 16, 16, 16, 6, 1, 1, 5, 29, 29, 38, 38, 1] 201 rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 20, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581341 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581341 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581341/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581341/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581341 Building REAL300025581342 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581342' /scratch/stefan/7787361/working/building/REAL300025581342 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581342 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581342/0 /scratch/stefan/7787361/working/building/REAL300025581342 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/857 `/scratch/stefan/7787361/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=CC(=O)NC=C21) `REAL300025581342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581342 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=CC(=O)NC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 54, 88, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 54, 54, 88, 88, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 546 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581342 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=CC(=O)NC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581342 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581342 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581342/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581342 Building REAL300025581343 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581343' /scratch/stefan/7787361/working/building/REAL300025581343 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581343 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581343/0 /scratch/stefan/7787361/working/building/REAL300025581343 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/858 `/scratch/stefan/7787361/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(SC(F)(F)F)N=C1) `REAL300025581343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581343 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(SC(F)(F)F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 5, 15, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 39, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 5, 17, 17, 17, 1, 1, 5, 29, 29, 39, 39, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 20, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26]) total number of confs: 361 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581343 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(SC(F)(F)F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 5, 15, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 67, 151, 151, 151, 151, 201, 201, 201, 201, 151, 151, 67, 17, 17, 8, 8, 151, 151, 151] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581343 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581343 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581343/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581343 Building REAL300025581344 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581344' /scratch/stefan/7787361/working/building/REAL300025581344 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581344 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581344/0 /scratch/stefan/7787361/working/building/REAL300025581344 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/859 `/scratch/stefan/7787361/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(N2CCOCC2)=N1) `REAL300025581344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581344 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(N2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 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: [61, 12, 61, 61, 113, 115, 168, 168, 168, 168, 168, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 61, 113, 113, 115, 115, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1] 168 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 503 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581344 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(N2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 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: [9, 1, 9, 9, 42, 47, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 9, 42, 42, 47, 47, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12] 168 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581344 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(N2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 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: [78, 78, 22, 8, 1, 1, 1, 1, 1, 1, 1, 78, 121, 121, 121, 121, 121, 168, 168, 168, 168, 168, 121, 77, 23, 23, 8, 8, 121, 121, 168, 168, 168, 168, 168, 168, 168, 168] 168 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581344 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581344 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581344/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581344 Building REAL300025581345 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581345' /scratch/stefan/7787361/working/building/REAL300025581345 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581345 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581345/0 /scratch/stefan/7787361/working/building/REAL300025581345 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/860 `/scratch/stefan/7787361/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC=C(F)C(Cl)=C2)=N1) `REAL300025581345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581345 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC=C(F)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 5, 29, 29, 91, 105, 201, 201, 201, 201, 201, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 29, 91, 91, 105, 105, 5, 1, 1, 1] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 562 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581345 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC=C(F)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 41, 54, 158, 158, 158, 158, 158, 1, 1, 1, 1, 1, 5, 5, 2, 2, 5, 5, 5, 1, 9, 40, 40, 54, 54, 1, 5, 5, 5] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 23, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581345 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2=CC=C(F)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 81, 158, 158, 158, 158, 201, 201, 201, 201, 201, 201, 201, 158, 81, 24, 24, 8, 8, 158, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 459 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581345 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581345 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581345/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581345 Building REAL300025581346 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581346' /scratch/stefan/7787361/working/building/REAL300025581346 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581346 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581346/0 /scratch/stefan/7787361/working/building/REAL300025581346 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/861 `/scratch/stefan/7787361/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581346 none CC(C)(C)OC(=O)N[C@H]1C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 166, 201, 119, 119, 119, 119, 45, 119, 45, 45, 17, 8, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 166, 119, 119, 45, 17, 17, 8, 8, 119, 119] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 678 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581346 none CC(C)(C)OC(=O)N[C@H]1C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 5, 9, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 41, 44, 119, 119, 119, 119, 119, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 8, 41, 41, 44, 44, 1, 1] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581346 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581346 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581346/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581346 Building REAL300025581347 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581347' /scratch/stefan/7787361/working/building/REAL300025581347 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581347 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581347/0 /scratch/stefan/7787361/working/building/REAL300025581347 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/862 `/scratch/stefan/7787361/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=C1Br)OCO2) `REAL300025581347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581347 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=C1Br)OCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 17, 12, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [7, 1, 7, 7, 43, 65, 146, 146, 146, 146, 146, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 43, 43, 65, 65, 1, 1, 1, 1] 146 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 394 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581347 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=C1Br)OCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 17, 12, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 23, 8, 1, 1, 1, 1, 1, 1, 1, 80, 146, 146, 146, 146, 146, 146, 146, 146, 146, 80, 23, 23, 8, 8, 146, 146, 146, 146] 146 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581347 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581347 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581347/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581347 Building REAL300025581348 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581348' /scratch/stefan/7787361/working/building/REAL300025581348 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581348 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581348/0 /scratch/stefan/7787361/working/building/REAL300025581348 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/863 `/scratch/stefan/7787361/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C(F)F)=CC=C1F) `REAL300025581348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581348 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 15, 15, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 54, 54, 157, 157, 157, 157, 157, 1, 1, 1, 1, 13, 13, 1, 1, 1, 1, 12, 54, 54, 54, 54, 1, 13, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 26, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 21, 22, 23, 24, 25, 27]) total number of confs: 361 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581348 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 15, 15, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 54, 157, 157, 157, 201, 201, 107, 157, 157, 157, 54, 17, 17, 8, 8, 157, 201, 157, 157] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 793 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581348 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581348 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581348/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581348 Building REAL300025581349 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581349' /scratch/stefan/7787361/working/building/REAL300025581349 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581349 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581349/0 /scratch/stefan/7787361/working/building/REAL300025581349 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/864 `/scratch/stefan/7787361/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C(=O)C2=CC=CC=C2)C1) `REAL300025581349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581349 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C(=O)C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 39, 39, 125, 126, 201, 201, 201, 201, 201, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 39, 125, 125, 126, 126, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 9, 9] 201 rigid atoms, others: [34, 35, 36, 37, 38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 598 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581349 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C(=O)C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 54, 57, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 5, 5, 9, 9, 7, 9, 9, 1, 9, 54, 54, 57, 57, 1, 1, 1, 1, 1, 9, 9, 8, 9, 9, 1, 1] 201 rigid atoms, others: [32, 1, 33, 40, 11, 12, 13, 14, 15, 23, 39, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38]) total number of confs: 370 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581349 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN(C(=O)C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 46, 159, 159, 159, 159, 201, 201, 201, 201, 201, 201, 201, 159, 46, 17, 17, 8, 8, 159, 159, 159, 159, 159, 201, 201, 201, 201, 201, 159, 159] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 624 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581349 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581349 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581349/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581349 Building REAL300025581350 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581350' /scratch/stefan/7787361/working/building/REAL300025581350 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581350 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581350/0 /scratch/stefan/7787361/working/building/REAL300025581350 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/865 `/scratch/stefan/7787361/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(SCC2=CC=CC=C2)=N1) `REAL300025581350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581350 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(SCC2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 14, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 69, 69, 69, 130, 130, 201, 201, 201, 201, 201, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 20, 20, 20, 69, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 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]) total number of confs: 614 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581350 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(SCC2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 14, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 15, 7, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 159, 201, 201, 201, 201, 201, 201, 94, 94, 94, 94, 39, 15, 15, 7, 7, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 571 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581350 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(SCC2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 14, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 35, 35, 94, 94, 94, 94, 94, 1, 1, 1, 5, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 7, 35, 35, 35, 35, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 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 /scratch/stefan/7787361/working/building/REAL300025581350 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581350 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581350/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581350 Building REAL300025581351 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581351' /scratch/stefan/7787361/working/building/REAL300025581351 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581351 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581351/0 /scratch/stefan/7787361/working/building/REAL300025581351 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/866 `/scratch/stefan/7787361/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)N(C2=CC=CC=C2)N=C1) `REAL300025581351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581351 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)N(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [33, 4, 33, 33, 102, 121, 196, 196, 196, 196, 196, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 33, 102, 102, 121, 121, 1, 1, 1, 1, 1, 4] 196 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 33]) total number of confs: 586 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581351 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)N(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 13, 69, 95, 196, 196, 196, 196, 196, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 13, 69, 69, 95, 95, 4, 4, 1, 4, 4, 1] 196 rigid atoms, others: [1, 33, 11, 12, 13, 14, 15, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 542 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581351 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)N(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 89, 196, 196, 196, 196, 196, 196, 196, 196, 196, 196, 196, 88, 24, 24, 8, 8, 196, 196, 196, 196, 196, 196] 196 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581351 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581351 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581351/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581351 Building REAL300025581352 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581352' /scratch/stefan/7787361/working/building/REAL300025581352 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581352 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581352/0 /scratch/stefan/7787361/working/building/REAL300025581352 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/867 `/scratch/stefan/7787361/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)C2=CC=CN=C2S1) `REAL300025581352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581352 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)C2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [7, 1, 7, 7, 43, 83, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 43, 43, 83, 83, 1, 1, 1] 155 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 495 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581352 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)C2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 81, 155, 155, 155, 155, 155, 155, 155, 155, 155, 81, 24, 24, 8, 8, 155, 155, 155] 155 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581352 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581352 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581352/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581352 Building REAL300025581353 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581353' /scratch/stefan/7787361/working/building/REAL300025581353 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581353 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581353/0 /scratch/stefan/7787361/working/building/REAL300025581353 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/868 `/scratch/stefan/7787361/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=NC=CS1) `REAL300025581353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581353 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=NC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 24, 24, 75, 88, 185, 185, 185, 185, 185, 6, 6, 6, 3, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 25, 25, 24, 75, 75, 88, 88, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6, 6, 25, 25] 201 rigid atoms, others: [40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48]) total number of confs: 534 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581353 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=NC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 38, 109, 109, 109, 109, 109, 1, 1, 1, 1, 1, 1, 5, 6, 6, 5, 6, 6, 1, 1, 1, 1, 9, 9, 9, 9, 7, 29, 29, 38, 38, 1, 1, 5, 5, 6, 6, 5, 6, 6, 1, 1, 9, 9] 201 rigid atoms, others: [1, 45, 36, 37, 11, 12, 13, 14, 15, 16, 46, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581353 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=NC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 17, 9, 1, 1, 1, 1, 1, 1, 1, 68, 109, 109, 109, 109, 109, 184, 185, 185, 184, 185, 185, 109, 109, 109, 109, 132, 132, 132, 132, 68, 17, 17, 9, 9, 109, 109, 184, 184, 185, 185, 184, 185, 185, 109, 109, 132, 132] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 778 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581353 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=NC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 9, 22, 22, 60, 70, 132, 132, 132, 132, 132, 9, 9, 9, 9, 9, 9, 23, 25, 25, 23, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 22, 60, 60, 70, 70, 9, 9, 23, 23, 25, 25, 23, 25, 25, 9, 9, 1, 1] 201 rigid atoms, others: [47, 48, 24, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 457 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581353 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581353/1 /scratch/stefan/7787361/working/building/REAL300025581353 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/869 `/scratch/stefan/7787361/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=NC=CS1) `REAL300025581353.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581353 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=NC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [29, 9, 29, 29, 52, 55, 94, 94, 94, 94, 94, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 29, 29, 29, 29, 29, 52, 52, 55, 55, 9, 9, 3, 3, 1, 1, 1, 1, 1, 9, 9, 29, 29] 105 rigid atoms, others: [40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48]) total number of confs: 308 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581353 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=NC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 18, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 7, 9, 9, 8, 9, 9, 1, 1, 1, 1, 7, 7, 7, 7, 6, 15, 15, 18, 18, 1, 1, 7, 7, 9, 9, 8, 9, 9, 1, 1, 7, 7] 105 rigid atoms, others: [1, 45, 36, 37, 11, 12, 13, 14, 15, 16, 46, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581353 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=NC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 15, 8, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 92, 94, 94, 93, 94, 94, 50, 50, 50, 50, 70, 70, 70, 70, 37, 15, 15, 8, 8, 50, 50, 92, 92, 94, 94, 93, 94, 94, 50, 50, 70, 70] 105 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 410 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581353 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=NC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 18, 18, 33, 35, 70, 70, 70, 70, 70, 7, 7, 7, 7, 7, 7, 27, 29, 29, 28, 29, 29, 7, 1, 7, 1, 1, 1, 1, 1, 18, 33, 33, 35, 35, 7, 7, 27, 27, 29, 29, 28, 29, 29, 7, 7, 1, 1] 105 rigid atoms, others: [47, 48, 24, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 285 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581353 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581353 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581353/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581353/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581353 Building REAL300025581354 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581354' /scratch/stefan/7787361/working/building/REAL300025581354 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581354 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581354/0 /scratch/stefan/7787361/working/building/REAL300025581354 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/870 `/scratch/stefan/7787361/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=NC=C1) `REAL300025581354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581354 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 24, 24, 71, 92, 178, 178, 178, 178, 178, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 24, 71, 71, 92, 92, 7, 7, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 178 rigid atoms, others: [41, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 50, 51]) total number of confs: 538 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581354 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 30, 43, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 1, 1, 2, 2, 1, 2, 2, 7, 30, 30, 43, 43, 1, 1, 5, 5, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 2] 178 rigid atoms, others: [1, 37, 38, 11, 12, 13, 14, 15, 16, 46, 23, 24, 25, 26, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581354 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 17, 8, 1, 1, 1, 1, 1, 1, 1, 65, 107, 107, 107, 107, 107, 178, 178, 178, 178, 178, 178, 107, 107, 107, 107, 107, 107, 107, 107, 107, 65, 17, 17, 8, 8, 107, 107, 178, 178, 178, 178, 178, 178, 178, 107, 107, 107, 107, 107, 107] 178 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581354 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 7, 30, 43, 107, 107, 107, 107, 107, 2, 2, 2, 2, 2, 2, 5, 7, 7, 6, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 30, 30, 43, 43, 2, 2, 5, 5, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1] 178 rigid atoms, others: [48, 49, 50, 51, 24, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 303 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581354 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581354/1 /scratch/stefan/7787361/working/building/REAL300025581354 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/871 `/scratch/stefan/7787361/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=NC=C1) `REAL300025581354.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581354 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 21, 21, 67, 74, 140, 140, 140, 140, 140, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 67, 67, 74, 74, 8, 8, 3, 3, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8] 140 rigid atoms, others: [41, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 50, 51]) total number of confs: 407 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581354 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 26, 34, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 6, 8, 8, 7, 8, 8, 1, 1, 1, 1, 2, 2, 1, 2, 2, 6, 26, 26, 34, 34, 1, 1, 6, 6, 8, 8, 8, 8, 8, 1, 1, 2, 2, 2, 2] 140 rigid atoms, others: [1, 37, 38, 11, 12, 13, 14, 15, 16, 46, 23, 24, 25, 26, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581354 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 15, 8, 1, 1, 1, 1, 1, 1, 1, 64, 92, 92, 92, 92, 92, 140, 140, 140, 140, 140, 140, 92, 92, 92, 92, 92, 92, 92, 92, 92, 64, 15, 15, 8, 8, 92, 92, 140, 140, 140, 140, 140, 140, 140, 92, 92, 92, 92, 92, 92] 140 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 567 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581354 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 26, 34, 92, 92, 92, 92, 92, 2, 2, 2, 2, 2, 2, 6, 8, 8, 7, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 26, 26, 34, 34, 2, 2, 6, 6, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1] 140 rigid atoms, others: [48, 49, 50, 51, 24, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 245 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581354 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581354 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581354/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581354/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581354 Building REAL300025581355 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581355' /scratch/stefan/7787361/working/building/REAL300025581355 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581355 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581355/0 /scratch/stefan/7787361/working/building/REAL300025581355 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/872 `/scratch/stefan/7787361/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581355 none CC(C)C[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 99, 99, 99, 99, 99, 99, 99, 150, 154, 154, 150, 154, 154, 99, 51, 99, 51, 52, 8, 8, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 113, 113, 113, 113, 99, 99, 150, 150, 154, 154, 150, 154, 154, 99, 99, 51, 8, 8, 8, 8] 156 rigid atoms, others: [23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 614 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581355 none CC(C)C[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 11, 11, 11, 11, 3, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 32, 32, 32, 87, 87, 154, 154, 154, 154, 154, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 11, 3, 3, 1, 1, 1, 1, 1, 11, 11, 32, 87, 87, 87, 87] 156 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 15, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 507 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581355 none CC(C)C[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 7, 11, 11, 1, 1, 1, 1, 6, 6, 6, 34, 34, 99, 99, 99, 99, 99, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 7, 7, 11, 11, 7, 11, 11, 1, 1, 6, 34, 34, 34, 34] 156 rigid atoms, others: [48, 3, 4, 5, 6, 7, 40, 9, 39, 16, 17, 18, 19, 8, 49] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53, 54]) total number of confs: 254 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581355 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581355/1 /scratch/stefan/7787361/working/building/REAL300025581355 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/873 `/scratch/stefan/7787361/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581355.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581355 none CC(C)C[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 115, 115, 115, 115, 115, 115, 115, 195, 198, 198, 197, 198, 198, 115, 44, 115, 44, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 129, 129, 129, 129, 115, 115, 195, 195, 198, 198, 198, 198, 198, 115, 115, 43, 8, 8, 8, 8] 201 rigid atoms, others: [23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 800 number of broken/clashed sets: 50 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581355 none CC(C)C[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 20, 9, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 30, 30, 30, 89, 89, 198, 198, 198, 198, 198, 20, 20, 20, 20, 20, 20, 20, 18, 18, 9, 9, 3, 3, 1, 1, 1, 1, 1, 9, 9, 30, 89, 89, 89, 89] 201 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 15, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 553 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581355 none CC(C)C[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 8, 9, 9, 1, 1, 1, 1, 8, 8, 8, 38, 38, 115, 115, 115, 115, 115, 5, 5, 5, 5, 5, 5, 5, 4, 4, 1, 1, 6, 6, 9, 9, 9, 9, 9, 1, 1, 8, 38, 38, 38, 38] 201 rigid atoms, others: [48, 3, 4, 5, 6, 7, 40, 9, 39, 16, 17, 18, 19, 8, 49] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53, 54]) total number of confs: 282 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581355 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581355 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581355/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581355/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581355 Building REAL300025581356 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581356' /scratch/stefan/7787361/working/building/REAL300025581356 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581356 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581356/0 /scratch/stefan/7787361/working/building/REAL300025581356 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/874 `/scratch/stefan/7787361/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=CC(OC)=C1O) `REAL300025581356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581356 none COC1=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 169, 169, 169, 169, 157, 38, 38, 38, 15, 7, 1, 1, 1, 1, 1, 1, 1, 169, 169, 169, 201, 169, 169, 201, 201, 201, 169, 169, 169, 157, 157, 38, 15, 15, 7, 7, 169, 201, 201, 201, 338] 402 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, 37, 38, 39, 40, 41]) total number of confs: 1134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581356 none COC1=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 7, 23, 23, 23, 93, 94, 197, 197, 197, 197, 197, 1, 1, 1, 3, 1, 1, 4, 4, 4, 1, 3, 3, 7, 7, 23, 94, 94, 94, 94, 1, 3, 3, 3, 2] 402 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 22, 23, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 526 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581356 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581356 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581356/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581356 Building REAL300025581357 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581357' /scratch/stefan/7787361/working/building/REAL300025581357 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581357 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581357/0 /scratch/stefan/7787361/working/building/REAL300025581357 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/875 `/scratch/stefan/7787361/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC[C@@H]1CC[C@H](C(F)(F)F)O1)NCCC1=NC(=O)O[N-]1) `REAL300025581357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581357 none O=C(CC[C@@H]1CC[C@H](C(F)(F)F)O1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 131, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 174, 174, 201, 201, 201, 201, 56, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 958 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581357 none O=C(CC[C@@H]1CC[C@H](C(F)(F)F)O1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 38, 38, 105, 108, 201, 201, 201, 201, 201, 10, 10, 7, 7, 1, 1, 1, 1, 38, 105, 105, 108, 108] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 14, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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/7787361/working/building/REAL300025581357 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581357 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581357/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581357 Building REAL300025581358 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581358' /scratch/stefan/7787361/working/building/REAL300025581358 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581358 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581358/0 /scratch/stefan/7787361/working/building/REAL300025581358 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/876 `/scratch/stefan/7787361/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC=C2N1CC1=CC=NC=C1) `REAL300025581358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581358 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC=C2N1CC1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 11, 30, 30, 95, 108, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 30, 95, 95, 108, 108, 11, 11, 11, 11, 11, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 595 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581358 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC=C2N1CC1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 41, 53, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 7, 11, 11, 10, 41, 41, 53, 53, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11] 201 rigid atoms, others: [32, 1, 34, 35, 36, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42]) total number of confs: 368 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581358 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC=C2N1CC1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 18, 8, 1, 1, 1, 1, 1, 1, 1, 57, 134, 134, 134, 134, 134, 134, 134, 134, 134, 179, 201, 201, 201, 201, 201, 57, 18, 18, 8, 8, 134, 134, 134, 134, 134, 179, 179, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581358 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581358 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581358/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581358 Building REAL300025581359 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581359' /scratch/stefan/7787361/working/building/REAL300025581359 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581359 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581359/0 /scratch/stefan/7787361/working/building/REAL300025581359 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/877 `/scratch/stefan/7787361/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CC=N1) `REAL300025581359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581359 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 7, 31, 31, 93, 103, 201, 201, 201, 201, 201, 7, 7, 7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 17, 31, 93, 93, 103, 103, 7, 7, 4, 4, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17] 201 rigid atoms, others: [41, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 50, 51]) total number of confs: 586 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581359 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 35, 41, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 5, 7, 7, 5, 7, 7, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 35, 35, 41, 41, 1, 1, 5, 5, 7, 7, 5, 7, 7, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [1, 37, 38, 11, 12, 13, 14, 15, 16, 46, 23, 24, 25, 26, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581359 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 17, 9, 1, 1, 1, 1, 1, 1, 1, 72, 119, 119, 119, 119, 119, 201, 201, 201, 201, 201, 201, 119, 119, 119, 119, 125, 125, 125, 125, 125, 72, 17, 17, 9, 9, 119, 119, 201, 201, 201, 201, 201, 201, 201, 119, 119, 125, 125, 125, 125] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 833 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581359 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 5, 18, 18, 58, 65, 125, 125, 125, 125, 125, 5, 5, 5, 5, 5, 5, 15, 17, 17, 15, 17, 17, 5, 1, 5, 1, 1, 1, 1, 1, 1, 18, 58, 58, 65, 65, 5, 5, 15, 15, 17, 17, 15, 17, 17, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [48, 49, 50, 51, 24, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 403 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581359 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581359/1 /scratch/stefan/7787361/working/building/REAL300025581359 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/878 `/scratch/stefan/7787361/working/3D/878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CC=N1) `REAL300025581359.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581359 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [29, 9, 29, 29, 63, 67, 122, 122, 122, 122, 122, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 23, 23, 23, 23, 23, 29, 63, 63, 67, 67, 9, 9, 3, 3, 1, 1, 1, 1, 1, 9, 9, 23, 23, 23, 23] 123 rigid atoms, others: [41, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 50, 51]) total number of confs: 377 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581359 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 24, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 6, 6, 7, 21, 21, 24, 24, 1, 1, 7, 7, 9, 9, 9, 9, 9, 1, 1, 6, 6, 6, 6] 123 rigid atoms, others: [1, 37, 38, 11, 12, 13, 14, 15, 16, 46, 23, 24, 25, 26, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581359 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 15, 8, 1, 1, 1, 1, 1, 1, 1, 39, 62, 62, 62, 62, 62, 117, 122, 122, 122, 122, 122, 62, 62, 62, 62, 80, 80, 80, 80, 80, 39, 15, 15, 8, 8, 62, 62, 117, 117, 122, 122, 122, 122, 122, 62, 62, 80, 80, 80, 80] 123 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 515 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581359 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 21, 39, 41, 80, 80, 80, 80, 80, 6, 6, 6, 6, 6, 6, 21, 23, 23, 23, 23, 23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 39, 39, 41, 41, 6, 6, 21, 21, 23, 23, 23, 23, 23, 6, 6, 1, 1, 1, 1] 123 rigid atoms, others: [48, 49, 50, 51, 24, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 279 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581359 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581359 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581359/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581359/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581359 Building REAL300025581360 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581360' /scratch/stefan/7787361/working/building/REAL300025581360 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581360 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581360/0 /scratch/stefan/7787361/working/building/REAL300025581360 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/879 `/scratch/stefan/7787361/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581360 none CCC[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 130, 91, 91, 91, 91, 91, 91, 91, 155, 161, 161, 155, 161, 161, 91, 48, 91, 48, 48, 8, 8, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 130, 130, 91, 91, 155, 155, 161, 161, 155, 161, 161, 91, 91, 47, 8, 8, 8, 8] 201 rigid atoms, others: [22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 863 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581360 none CCC[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 9, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 27, 27, 66, 66, 161, 161, 161, 161, 161, 26, 26, 26, 26, 26, 22, 22, 9, 9, 3, 3, 1, 1, 1, 1, 1, 9, 9, 27, 66, 66, 66, 66] 201 rigid atoms, others: [43, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 42] 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, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 456 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581360 none CCC[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 6, 9, 9, 1, 1, 1, 1, 6, 6, 6, 28, 28, 91, 91, 91, 91, 91, 7, 7, 7, 7, 7, 5, 5, 1, 1, 6, 6, 9, 9, 6, 9, 9, 1, 1, 6, 28, 28, 28, 28] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 45, 46, 15, 16, 17, 18, 36, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 235 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581360 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581360/1 /scratch/stefan/7787361/working/building/REAL300025581360 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/880 `/scratch/stefan/7787361/working/3D/880' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581360.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581360 none CCC[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 143, 114, 114, 114, 114, 114, 114, 114, 189, 194, 194, 189, 194, 194, 114, 48, 114, 48, 48, 9, 9, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 144, 143, 143, 114, 114, 189, 189, 194, 194, 189, 194, 194, 114, 114, 48, 9, 9, 9, 9] 201 rigid atoms, others: [22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 885 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: REAL300025581360 none CCC[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 18, 8, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 28, 28, 88, 88, 194, 194, 194, 194, 194, 27, 27, 27, 27, 27, 18, 18, 8, 8, 3, 3, 1, 1, 1, 1, 1, 8, 8, 28, 88, 88, 88, 88] 201 rigid atoms, others: [43, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 42] 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, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 565 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581360 none CCC[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 6, 8, 8, 1, 1, 1, 1, 8, 8, 8, 37, 37, 114, 114, 114, 114, 114, 8, 8, 8, 8, 8, 5, 5, 1, 1, 6, 6, 8, 8, 6, 8, 8, 1, 1, 8, 37, 37, 37, 37] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 45, 46, 15, 16, 17, 18, 36, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 287 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581360 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581360 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581360/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581360/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581360 Building REAL300025581361 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581361' /scratch/stefan/7787361/working/building/REAL300025581361 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581361 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581361/0 /scratch/stefan/7787361/working/building/REAL300025581361 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/881 `/scratch/stefan/7787361/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1CCCC1) `REAL300025581361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581361 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 7, 26, 26, 89, 103, 188, 188, 188, 188, 188, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 14, 26, 89, 89, 103, 103, 7, 7, 3, 3, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14] 201 rigid atoms, others: [40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 569 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581361 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 32, 41, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 5, 7, 7, 5, 7, 7, 1, 1, 1, 1, 5, 5, 5, 5, 7, 32, 32, 41, 41, 1, 1, 5, 5, 7, 7, 5, 7, 7, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 45, 36, 37, 11, 12, 13, 14, 15, 16, 46, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 292 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581361 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 1, 1, 1, 1, 1, 1, 1, 63, 107, 107, 107, 107, 107, 188, 188, 188, 188, 188, 188, 107, 107, 107, 107, 119, 119, 119, 119, 63, 17, 17, 9, 9, 107, 107, 188, 188, 188, 188, 188, 188, 188, 107, 107, 119, 119, 119, 119, 119, 119, 119, 119, 119] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 826 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581361 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 13, 46, 55, 119, 119, 119, 119, 119, 5, 5, 5, 5, 5, 5, 12, 14, 14, 12, 14, 14, 5, 1, 5, 1, 1, 1, 1, 1, 13, 46, 46, 55, 55, 5, 5, 12, 12, 14, 14, 12, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [47, 48, 49, 50, 51, 52, 53, 54, 55, 24, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 358 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581361 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581361/1 /scratch/stefan/7787361/working/building/REAL300025581361 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/882 `/scratch/stefan/7787361/working/3D/882' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1CCCC1) `REAL300025581361.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581361 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [32, 9, 32, 32, 69, 71, 118, 118, 118, 118, 118, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 16, 16, 16, 16, 32, 69, 69, 71, 71, 9, 9, 3, 3, 1, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16] 120 rigid atoms, others: [40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 383 number of broken/clashed sets: 31 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581361 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 26, 29, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 7, 9, 9, 8, 9, 9, 1, 1, 1, 1, 4, 4, 4, 4, 8, 26, 26, 29, 29, 1, 1, 7, 7, 9, 9, 7, 9, 9, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 120 rigid atoms, others: [1, 45, 36, 37, 11, 12, 13, 14, 15, 16, 46, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 213 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581361 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 16, 9, 1, 1, 1, 1, 1, 1, 1, 54, 76, 76, 76, 76, 76, 117, 118, 118, 117, 118, 118, 76, 76, 76, 76, 84, 84, 84, 84, 54, 16, 16, 9, 9, 76, 76, 117, 117, 118, 118, 117, 118, 118, 76, 76, 84, 84, 84, 84, 84, 84, 84, 84, 84] 120 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 500 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581361 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 13, 13, 33, 36, 84, 84, 84, 84, 84, 4, 4, 4, 4, 4, 4, 14, 16, 16, 14, 16, 16, 4, 1, 4, 1, 1, 1, 1, 1, 13, 33, 33, 36, 36, 4, 4, 14, 14, 16, 16, 14, 16, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 120 rigid atoms, others: [47, 48, 49, 50, 51, 52, 53, 54, 55, 24, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 259 number of broken/clashed sets: 31 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581361 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581361 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581361/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581361/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581361 Building REAL300025581362 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581362' /scratch/stefan/7787361/working/building/REAL300025581362 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025581362 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581362/0 /scratch/stefan/7787361/working/building/REAL300025581362 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/883 `/scratch/stefan/7787361/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CS1) `REAL300025581362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581362 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 7, 27, 27, 77, 89, 173, 173, 173, 173, 173, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 27, 77, 77, 89, 89, 7, 7, 3, 3, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17] 201 rigid atoms, others: [40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49]) total number of confs: 511 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581362 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 26, 33, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 1, 5, 7, 7, 5, 7, 7, 1, 1, 1, 1, 6, 6, 6, 6, 7, 26, 26, 33, 33, 1, 1, 5, 5, 7, 7, 5, 7, 7, 1, 1, 6, 6, 6] 201 rigid atoms, others: [1, 45, 36, 37, 11, 12, 13, 14, 15, 16, 46, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 253 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581362 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 17, 8, 1, 1, 1, 1, 1, 1, 1, 67, 96, 96, 96, 96, 96, 173, 173, 173, 173, 173, 173, 96, 96, 96, 96, 118, 118, 118, 118, 67, 17, 17, 8, 8, 96, 96, 173, 173, 173, 173, 173, 173, 173, 96, 96, 118, 118, 118] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 765 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581362 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 15, 42, 51, 118, 118, 118, 118, 118, 6, 6, 6, 6, 6, 6, 15, 17, 17, 15, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 15, 42, 42, 51, 51, 6, 6, 15, 15, 17, 17, 15, 17, 17, 6, 6, 1, 1, 1] 201 rigid atoms, others: [47, 48, 49, 24, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 359 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581362 /scratch/stefan/7787361/working /scratch/stefan/7787361 mkdir: created directory `1' /scratch/stefan/7787361/working/building/REAL300025581362/1 /scratch/stefan/7787361/working/building/REAL300025581362 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/884 `/scratch/stefan/7787361/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CS1) `REAL300025581362.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025581362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581362 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [24, 9, 24, 24, 44, 48, 84, 84, 84, 84, 84, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 21, 21, 21, 21, 24, 44, 44, 48, 48, 9, 9, 3, 3, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21] 103 rigid atoms, others: [40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49]) total number of confs: 267 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581362 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 18, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 7, 9, 9, 8, 9, 9, 1, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 18, 18, 1, 1, 7, 7, 9, 9, 8, 9, 9, 1, 1, 6, 6, 6] 103 rigid atoms, others: [1, 45, 36, 37, 11, 12, 13, 14, 15, 16, 46, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581362 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 16, 9, 1, 1, 1, 1, 1, 1, 1, 36, 48, 48, 48, 48, 48, 84, 84, 84, 84, 84, 84, 48, 48, 48, 48, 64, 64, 64, 64, 36, 16, 16, 8, 8, 48, 48, 84, 84, 84, 84, 84, 84, 84, 48, 48, 64, 64, 64] 103 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581362 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[N@@H+](CC2=CC=CC=C2)C[C@H]1C1=CC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 14, 27, 29, 64, 64, 64, 64, 64, 6, 6, 6, 6, 6, 6, 19, 21, 21, 20, 21, 21, 6, 1, 6, 1, 1, 1, 1, 1, 14, 27, 27, 29, 29, 6, 6, 19, 19, 21, 21, 20, 21, 21, 6, 6, 1, 1, 1] 103 rigid atoms, others: [47, 48, 49, 24, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 231 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581362 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581362 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 1: /scratch/stefan/7787361/working/building/REAL300025581362/1.* 0: /scratch/stefan/7787361/working/building/REAL300025581362/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581362 Building REAL300025581363 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581363' /scratch/stefan/7787361/working/building/REAL300025581363 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581363 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581363/0 /scratch/stefan/7787361/working/building/REAL300025581363 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/885 `/scratch/stefan/7787361/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=C(F)C=C2)N=C1) `REAL300025581363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581363 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=C(F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 16, 40, 40, 112, 114, 201, 201, 201, 201, 201, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 40, 112, 112, 114, 114, 16, 16, 1, 1, 1, 1, 16] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 569 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581363 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=C(F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 21, 23, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 8, 16, 16, 8, 8, 16, 16, 1, 1, 5, 21, 21, 23, 23, 1, 1, 16, 16, 16, 16, 1] 201 rigid atoms, others: [1, 36, 11, 12, 13, 14, 15, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581363 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=C(F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 17, 8, 1, 1, 1, 1, 1, 1, 1, 38, 66, 66, 66, 66, 198, 201, 201, 198, 198, 201, 201, 66, 66, 38, 17, 17, 8, 8, 66, 66, 201, 201, 201, 201, 66] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581363 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581363 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581363/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581363 Building REAL300025581364 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581364' /scratch/stefan/7787361/working/building/REAL300025581364 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581364 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581364/0 /scratch/stefan/7787361/working/building/REAL300025581364 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/886 `/scratch/stefan/7787361/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2CCCC2)=C1) `REAL300025581364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581364 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 17, 84, 94, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 17, 84, 84, 94, 94, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 30, 31] 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, 38]) total number of confs: 523 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581364 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 37, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 5, 29, 29, 37, 37, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1] 201 rigid atoms, others: [1, 38, 11, 12, 13, 14, 15, 16, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581364 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 19, 8, 1, 1, 1, 1, 1, 1, 1, 55, 117, 117, 117, 117, 117, 201, 201, 201, 201, 117, 55, 19, 19, 8, 8, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 117] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581364 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581364 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581364/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581364 Building REAL300025581365 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581365' /scratch/stefan/7787361/working/building/REAL300025581365 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581365 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581365/0 /scratch/stefan/7787361/working/building/REAL300025581365 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/887 `/scratch/stefan/7787361/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1OC(C)C) `REAL300025581365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581365 none COC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 171, 171, 171, 171, 171, 91, 91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 171, 171, 195, 201, 201, 199, 199, 199, 171, 171, 171, 90, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201] 201 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, 37, 38, 39, 40]) total number of confs: 557 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581365 none COC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 30, 42, 171, 171, 171, 171, 171, 1, 1, 5, 13, 13, 4, 4, 4, 1, 1, 1, 8, 30, 30, 42, 42, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 18, 19, 26, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581365 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581365 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581365/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581365 Building REAL300025581366 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581366' /scratch/stefan/7787361/working/building/REAL300025581366 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581366 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581366/0 /scratch/stefan/7787361/working/building/REAL300025581366 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/888 `/scratch/stefan/7787361/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CC=C(Br)N2N=C1) `REAL300025581366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581366 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CC=C(Br)N2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 12, 67, 94, 192, 192, 192, 192, 192, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 67, 67, 94, 94, 1, 1, 1, 1] 192 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 535 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581366 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CC=C(Br)N2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 97, 192, 192, 192, 192, 192, 192, 192, 191, 191, 96, 24, 24, 8, 8, 192, 192, 192, 192] 192 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 443 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581366 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581366 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581366/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581366 Building REAL300025581367 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581367' /scratch/stefan/7787361/working/building/REAL300025581367 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581367 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581367/0 /scratch/stefan/7787361/working/building/REAL300025581367 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/889 `/scratch/stefan/7787361/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=CC=C2F)N=C1) `REAL300025581367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581367 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=CC=C2F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 22, 49, 49, 122, 122, 201, 201, 201, 201, 201, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 49, 122, 122, 122, 122, 22, 22, 1, 1, 1, 1, 22] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 596 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581367 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=CC=C2F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 18, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 8, 22, 22, 12, 22, 22, 22, 1, 1, 5, 16, 16, 18, 18, 1, 1, 22, 22, 20, 22, 1] 201 rigid atoms, others: [1, 36, 11, 12, 13, 14, 15, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581367 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OC2=CC=CC=C2F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 15, 7, 1, 1, 1, 1, 1, 1, 1, 32, 58, 58, 58, 58, 145, 201, 201, 197, 201, 201, 201, 58, 58, 32, 15, 15, 7, 7, 58, 58, 201, 201, 201, 201, 58] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581367 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581367 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581367/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581367 Building REAL300025581368 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581368' /scratch/stefan/7787361/working/building/REAL300025581368 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581368 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581368/0 /scratch/stefan/7787361/working/building/REAL300025581368 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/890 `/scratch/stefan/7787361/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C(=C1)NC(=O)N2C1CC1) `REAL300025581368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581368 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C(=C1)NC(=O)N2C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 19, 82, 109, 201, 201, 201, 201, 201, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 19, 82, 82, 109, 109, 6, 6, 6, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 580 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581368 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C(=C1)NC(=O)N2C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 45, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 5, 29, 29, 45, 45, 1, 1, 1, 1, 6, 6, 6, 6, 6] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 311 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581368 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C(=C1)NC(=O)N2C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 1, 1, 1, 1, 1, 1, 1, 61, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 201, 201, 60, 21, 21, 8, 8, 127, 127, 127, 127, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 601 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581368 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581368 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581368/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581368 Building REAL300025581369 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581369' /scratch/stefan/7787361/working/building/REAL300025581369 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581369 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581369/0 /scratch/stefan/7787361/working/building/REAL300025581369 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/891 `/scratch/stefan/7787361/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(NC2=CC=CN=C2)C=C1) `REAL300025581369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581369 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(NC2=CC=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 25, 45, 45, 119, 119, 201, 201, 201, 201, 201, 13, 25, 25, 13, 1, 1, 1, 1, 1, 1, 1, 25, 25, 45, 119, 119, 119, 119, 25, 25, 13, 1, 1, 1, 1, 25, 25] 201 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37]) total number of confs: 679 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581369 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(NC2=CC=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 15, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 13, 25, 25, 25, 25, 25, 1, 1, 3, 13, 13, 15, 15, 1, 1, 13, 25, 25, 25, 25, 1, 1] 201 rigid atoms, others: [1, 36, 37, 11, 12, 13, 14, 15, 22, 23, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581369 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(NC2=CC=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 15, 7, 1, 1, 1, 1, 1, 1, 1, 32, 47, 47, 47, 47, 167, 201, 201, 201, 201, 201, 47, 47, 32, 15, 15, 7, 7, 47, 47, 167, 201, 201, 201, 201, 47, 47] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 527 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581369 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581369 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581369/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581369 Building REAL300025581370 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581370' /scratch/stefan/7787361/working/building/REAL300025581370 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581370 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581370/0 /scratch/stefan/7787361/working/building/REAL300025581370 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/892 `/scratch/stefan/7787361/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=NC(C(F)(F)F)=CN2C=C1) `REAL300025581370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581370 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=NC(C(F)(F)F)=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 5, 15, 15, 15, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 41, 63, 118, 118, 118, 118, 118, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 41, 41, 63, 63, 1, 1, 1, 1] 118 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581370 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=NC(C(F)(F)F)=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 5, 15, 15, 15, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 21, 8, 1, 1, 1, 1, 1, 1, 1, 73, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 72, 21, 22, 8, 8, 118, 118, 118, 118] 118 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581370 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581370 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581370/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581370 Building REAL300025581371 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581371' /scratch/stefan/7787361/working/building/REAL300025581371 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581371 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581371/0 /scratch/stefan/7787361/working/building/REAL300025581371 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/893 `/scratch/stefan/7787361/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2C[C@@H](C(=O)NCCC3=NC(=O)O[N-]3)[C@@H]2C1) `REAL300025581371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581371 none CC(C)(C)OC(=O)N1C[C@@H]2C[C@@H](C(=O)NCCC3=NC(=O)O[N-]3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 160, 114, 160, 114, 114, 114, 114, 114, 44, 114, 44, 44, 17, 8, 1, 1, 1, 1, 1, 1, 1, 114, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 114, 114, 114, 114, 44, 17, 17, 8, 8, 114, 114] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 601 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581371 none CC(C)(C)OC(=O)N1C[C@@H]2C[C@@H](C(=O)NCCC3=NC(=O)O[N-]3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 8, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 44, 45, 114, 114, 114, 114, 114, 1, 1, 1, 10, 10, 10, 9, 9, 9, 10, 10, 10, 1, 1, 1, 1, 10, 44, 44, 45, 45, 1, 1] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 47, 40, 46, 25, 26, 27, 39, 5] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581371 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581371 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581371/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581371 Building REAL300025581372 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581372' /scratch/stefan/7787361/working/building/REAL300025581372 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581372 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581372/0 /scratch/stefan/7787361/working/building/REAL300025581372 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/894 `/scratch/stefan/7787361/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(F)=C1Cl) `REAL300025581372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581372 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(F)=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 15, 1, 16, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 42, 58, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 42, 42, 58, 58, 1, 1] 145 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 372 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581372 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(F)=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 15, 1, 16, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 22, 8, 1, 1, 1, 1, 1, 1, 1, 70, 145, 145, 145, 145, 145, 145, 145, 145, 70, 22, 22, 8, 8, 145, 145] 145 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581372 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581372 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581372/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581372 Building REAL300025581373 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581373' /scratch/stefan/7787361/working/building/REAL300025581373 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581373 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581373/0 /scratch/stefan/7787361/working/building/REAL300025581373 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/895 `/scratch/stefan/7787361/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(CCC(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581373 none CC(C)(C)OC(=O)N1CCCC(CCC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 190, 131, 190, 131, 131, 131, 131, 91, 94, 27, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 131, 131, 131, 131, 131, 131, 100, 100, 95, 95, 26, 9, 8, 8, 8, 131, 131] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 782 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581373 none CC(C)(C)OC(=O)N1CCCC(CCC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 7, 25, 25, 25, 67, 67, 131, 131, 131, 131, 131, 1, 6, 6, 6, 6, 5, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 25, 67, 67, 67, 67, 1, 1] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 51, 52, 41, 25, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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 /scratch/stefan/7787361/working/building/REAL300025581373 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581373 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581373/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581373 Building REAL300025581374 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581374' /scratch/stefan/7787361/working/building/REAL300025581374 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581374 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581374/0 /scratch/stefan/7787361/working/building/REAL300025581374 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/896 `/scratch/stefan/7787361/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581374 none CC(C)CCC(NC(=O)OC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 126, 126, 69, 22, 69, 107, 144, 144, 144, 144, 144, 144, 22, 22, 10, 7, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 69, 107, 144, 144, 144, 144, 144, 144, 144, 144, 144, 22, 10, 10, 7, 7] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 899 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581374 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581374 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581374/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581374 Building REAL300025581375 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581375' /scratch/stefan/7787361/working/building/REAL300025581375 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581375 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581375/0 /scratch/stefan/7787361/working/building/REAL300025581375 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/897 `/scratch/stefan/7787361/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)N1CCN(C(=O)OC(C)(C)C)CC1=O) `REAL300025581375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581375 none CC(C(=O)NCCC1=NC(=O)O[N-]1)N1CCN(C(=O)OC(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 13, 13, 13, 33, 34, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 5, 5, 15, 17, 17, 17, 1, 1, 1, 4, 4, 4, 4, 13, 33, 33, 34, 34, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201 rigid atoms, others: [1, 36, 37, 38, 39, 13, 14, 15, 16, 17, 50, 24, 25, 49, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 265 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581375 none CC(C(=O)NCCC1=NC(=O)O[N-]1)N1CCN(C(=O)OC(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 44, 17, 8, 1, 1, 1, 1, 1, 1, 1, 71, 86, 86, 86, 86, 137, 137, 201, 201, 201, 201, 86, 86, 86, 71, 71, 71, 71, 44, 17, 17, 8, 8, 86, 86, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 86] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 631 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581375 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581375 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581375/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581375 Building REAL300025581376 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581376' /scratch/stefan/7787361/working/building/REAL300025581376 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581376 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581376/0 /scratch/stefan/7787361/working/building/REAL300025581376 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/898 `/scratch/stefan/7787361/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NCCC1=NC(=O)O[N-]1)NC(=O)OC(C)(C)C) `REAL300025581376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581376 none C[C@@H](CC(=O)NCCC1=NC(=O)O[N-]1)NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 12, 5, 5, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 111, 135, 37, 38, 38, 8, 8, 1, 1, 1, 1, 1, 1, 1, 135, 161, 197, 197, 201, 201, 201, 201, 135, 135, 135, 110, 110, 37, 9, 9, 8, 8, 161, 201, 201, 201, 201, 201, 201, 201, 201, 201] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 863 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581376 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581376 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581376/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581376 Building REAL300025581377 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581377' /scratch/stefan/7787361/working/building/REAL300025581377 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581377 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581377/0 /scratch/stefan/7787361/working/building/REAL300025581377 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/899 `/scratch/stefan/7787361/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581377 none CC(C)(C)OC(=O)NC1CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 191, 179, 191, 124, 124, 124, 124, 43, 43, 43, 16, 8, 1, 1, 1, 1, 1, 1, 1, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 124, 124, 124, 124, 43, 16, 16, 8, 8, 124, 124] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 538 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581377 none CC(C)(C)OC(=O)NC1CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 11, 6, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 31, 36, 124, 124, 124, 124, 124, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 5, 31, 31, 36, 36, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581377 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581377 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581377/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581377 Building REAL300025581378 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581378' /scratch/stefan/7787361/working/building/REAL300025581378 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581378 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581378/0 /scratch/stefan/7787361/working/building/REAL300025581378 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/900 `/scratch/stefan/7787361/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CC=CO2)=N1) `REAL300025581378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581378 none CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CC=CO2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 34, 34, 34, 93, 99, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 34, 93, 93, 99, 99, 1, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 534 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581378 none CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CC=CO2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 65, 65, 65, 23, 8, 1, 1, 1, 1, 1, 1, 1, 173, 173, 201, 201, 201, 201, 173, 173, 173, 173, 173, 64, 24, 24, 8, 8, 201, 201, 201] 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: 422 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581378 none CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CC=CO2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 49, 59, 173, 173, 173, 173, 173, 1, 1, 12, 12, 12, 12, 1, 2, 2, 2, 1, 12, 49, 49, 59, 59, 12, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581378 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581378 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581378/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581378 Building REAL300025581379 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581379' /scratch/stefan/7787361/working/building/REAL300025581379 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581379 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581379/0 /scratch/stefan/7787361/working/building/REAL300025581379 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/901 `/scratch/stefan/7787361/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C(NC(=O)OC(C)(C)C)C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025581379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581379 none COC1=CC=CC(C(NC(=O)OC(C)(C)C)C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 125, 125, 125, 125, 125, 65, 36, 65, 94, 127, 127, 127, 127, 127, 127, 36, 36, 15, 7, 1, 1, 1, 1, 1, 1, 1, 125, 143, 143, 143, 125, 125, 125, 65, 94, 127, 127, 127, 127, 127, 127, 127, 127, 127, 36, 15, 15, 7, 7, 125] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 635 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581379 none COC1=CC=CC(C(NC(=O)OC(C)(C)C)C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 14, 22, 22, 22, 22, 22, 22, 7, 15, 15, 15, 49, 51, 125, 125, 125, 125, 125, 1, 3, 3, 3, 1, 1, 1, 7, 14, 22, 22, 22, 22, 22, 22, 22, 22, 22, 15, 49, 49, 51, 51, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 50, 27, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581379 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581379 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581379/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581379 Building REAL300025581380 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581380' /scratch/stefan/7787361/working/building/REAL300025581380 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581380 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581380/0 /scratch/stefan/7787361/working/building/REAL300025581380 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/902 `/scratch/stefan/7787361/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CN(C(=O)OC(C)(C)C)C(C)(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581380 none COC1CN(C(=O)OC(C)(C)C)C(C)(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 135, 135, 135, 135, 135, 175, 175, 201, 201, 201, 201, 48, 135, 48, 48, 8, 8, 1, 1, 1, 1, 1, 1, 1, 135, 155, 155, 155, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 135, 135, 47, 8, 8, 8, 8, 135, 135] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 608 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581380 none COC1CN(C(=O)OC(C)(C)C)C(C)(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 6, 6, 11, 12, 12, 12, 1, 1, 1, 9, 9, 9, 44, 44, 135, 135, 135, 135, 135, 1, 6, 6, 6, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 9, 44, 44, 44, 44, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 49, 50, 25, 29, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 305 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581380 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581380 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581380/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581380 Building REAL300025581381 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581381' /scratch/stefan/7787361/working/building/REAL300025581381 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581381 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581381/0 /scratch/stefan/7787361/working/building/REAL300025581381 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/903 `/scratch/stefan/7787361/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1(C(F)(F)F)CC1) `REAL300025581381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581381 none CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 18, 11, 18, 5, 1, 5, 10, 10, 10, 42, 45, 109, 109, 109, 109, 109, 1, 1, 2, 2, 2, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 5, 10, 42, 42, 45, 45, 1, 1, 1, 1] 201 rigid atoms, others: [8, 43, 44, 45, 46, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 334 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581381 none CC(C)(C)OC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C1(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 200, 200, 190, 149, 190, 96, 34, 34, 34, 15, 8, 1, 1, 1, 1, 1, 1, 1, 96, 109, 109, 109, 109, 109, 109, 200, 200, 200, 200, 200, 200, 200, 200, 200, 149, 96, 34, 15, 15, 8, 8, 109, 109, 109, 109] 201 rigid atoms, others: [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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 789 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581381 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581381 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581381/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581381 Building REAL300025581382 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581382' /scratch/stefan/7787361/working/building/REAL300025581382 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581382 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581382/0 /scratch/stefan/7787361/working/building/REAL300025581382 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/904 `/scratch/stefan/7787361/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2C[C@@H]2[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581382 none CC(C)(C)OC(=O)N1C[C@@H]2C[C@@H]2[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 132, 87, 132, 87, 87, 87, 87, 87, 87, 87, 58, 87, 58, 58, 20, 9, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 87, 87, 87, 58, 20, 20, 9, 9] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 590 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581382 none CC(C)(C)OC(=O)N1C[C@@H]2C[C@@H]2[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 24, 32, 87, 87, 87, 87, 87, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 5, 24, 24, 32, 32] 201 rigid atoms, others: [36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 39, 37] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581382 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581382 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581382/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581382 Building REAL300025581383 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581383' /scratch/stefan/7787361/working/building/REAL300025581383 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581383 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581383/0 /scratch/stefan/7787361/working/building/REAL300025581383 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/905 `/scratch/stefan/7787361/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NN(C)C=C2C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL300025581383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581383 none CC1=CC=C(C2=NN(C)C=C2C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 175, 175, 175, 175, 175, 175, 70, 70, 70, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 175, 175, 175, 175, 70, 23, 23, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 425 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581383 none CC1=CC=C(C2=NN(C)C=C2C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 58, 69, 175, 175, 175, 175, 175, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 13, 58, 58, 69, 69] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 446 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581383 none CC1=CC=C(C2=NN(C)C=C2C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 43, 43, 43, 99, 109, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 12, 12, 12, 12, 43, 99, 99, 109, 109] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 582 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581383 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581383 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581383/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581383 Building REAL300025581384 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581384' /scratch/stefan/7787361/working/building/REAL300025581384 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581384 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581384/0 /scratch/stefan/7787361/working/building/REAL300025581384 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/906 `/scratch/stefan/7787361/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1=CC=CC=C1) `REAL300025581384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581384 none CC1=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 10, 49, 49, 49, 134, 135, 201, 201, 201, 201, 201, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 10, 10, 49, 134, 134, 135, 135, 3, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 637 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581384 none CC1=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 27, 27, 27, 13, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 107, 27, 13, 13, 7, 7, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 550 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581384 none CC1=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 31, 31, 31, 98, 104, 201, 201, 201, 201, 201, 1, 1, 1, 1, 3, 3, 2, 3, 3, 2, 2, 2, 1, 6, 6, 31, 98, 98, 104, 104, 2, 2, 2, 3, 3, 2, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581384 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581384 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581384/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581384 Building REAL300025581385 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581385' /scratch/stefan/7787361/working/building/REAL300025581385 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581385 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581385/0 /scratch/stefan/7787361/working/building/REAL300025581385 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/907 `/scratch/stefan/7787361/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(N2C=NC3=CC(C(=O)NCCC4=NC(=O)O[N-]4)=CC=C32)=C1) `REAL300025581385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581385 none CC1=CC=CC(N2C=NC3=CC(C(=O)NCCC4=NC(=O)O[N-]4)=CC=C32)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 80, 201, 201, 80, 80, 80, 80, 80, 80, 38, 38, 38, 17, 8, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 201, 201, 201, 201, 80, 201, 201, 80, 80, 38, 17, 17, 8, 8, 80, 80, 201] 201 rigid atoms, others: [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]) total number of confs: 624 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581385 none CC1=CC=CC(N2C=NC3=CC(C(=O)NCCC4=NC(=O)O[N-]4)=CC=C32)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 25, 27, 80, 80, 80, 80, 80, 1, 1, 1, 9, 9, 9, 9, 1, 9, 9, 1, 1, 5, 25, 25, 27, 27, 1, 1, 9] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 11, 12, 34, 40, 41, 23, 24, 25] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581385 none CC1=CC=CC(N2C=NC3=CC(C(=O)NCCC4=NC(=O)O[N-]4)=CC=C32)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 27, 27, 27, 115, 119, 201, 201, 201, 201, 201, 9, 9, 9, 1, 2, 2, 2, 1, 1, 1, 9, 9, 27, 115, 115, 119, 119, 9, 9, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 42, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 585 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581385 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581385 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581385/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581385 Building REAL300025581386 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581386' /scratch/stefan/7787361/working/building/REAL300025581386 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581386 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581386/0 /scratch/stefan/7787361/working/building/REAL300025581386 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/908 `/scratch/stefan/7787361/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(F)(F)F)=NC2=CN=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C21) `REAL300025581386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581386 none CN1C(C(F)(F)F)=NC2=CN=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 5, 15, 15, 15, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 73, 73, 73, 24, 8, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 139, 139, 73, 25, 24, 8, 8] 139 rigid atoms, others: [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]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581386 none CN1C(C(F)(F)F)=NC2=CN=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 5, 15, 15, 15, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 65, 139, 139, 139, 139, 139, 1, 2, 2, 2, 1, 1, 9, 45, 45, 65, 65] 139 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 24, 28, 29] set([32, 33, 34, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581386 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581386 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581386/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581386 Building REAL300025581387 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581387' /scratch/stefan/7787361/working/building/REAL300025581387 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581387 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581387/0 /scratch/stefan/7787361/working/building/REAL300025581387 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/909 `/scratch/stefan/7787361/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCCC=CCCCCCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581387 none CCCCCCCCC=CCCCCCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 185, 185, 201, 201, 201, 201, 131, 131, 60, 52, 60, 52, 60, 52, 44, 8, 8, 8, 7, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 131, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 44, 44, 8, 7, 7, 5, 5] 201 rigid atoms, others: [21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 1182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581387 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581387 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581387/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581387 Building REAL300025581388 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581388' /scratch/stefan/7787361/working/building/REAL300025581388 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581388 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581388/0 /scratch/stefan/7787361/working/building/REAL300025581388 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/910 `/scratch/stefan/7787361/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)C=C1C) `REAL300025581388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581388 none CC1=CC=C([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 143, 143, 143, 143, 47, 143, 47, 47, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 47, 19, 19, 8, 8, 201, 201, 201, 201] 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]) total number of confs: 542 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581388 none CC1=CC=C([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 63, 65, 143, 143, 143, 143, 143, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 13, 63, 63, 65, 65, 7, 7, 7, 7] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 347 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581388 none CC1=CC=C([C@@H]2C[C@H]2C(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 29, 29, 29, 109, 110, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 29, 109, 109, 110, 110, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22, 23, 36, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 540 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581388 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581388 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581388/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581388 Building REAL300025581389 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581389' /scratch/stefan/7787361/working/building/REAL300025581389 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581389 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581389/0 /scratch/stefan/7787361/working/building/REAL300025581389 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/911 `/scratch/stefan/7787361/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(CC1=NC=CC=N1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581389 none CC(C)(C)OC(=O)NC(CC1=NC=CC=N1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 174, 157, 125, 157, 76, 47, 76, 93, 106, 106, 93, 106, 106, 47, 47, 19, 8, 1, 1, 1, 1, 1, 1, 1, 174, 174, 174, 174, 174, 174, 174, 174, 174, 125, 76, 93, 93, 106, 93, 106, 47, 19, 19, 8, 8] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 804 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581389 none CC(C)(C)OC(=O)NC(CC1=NC=CC=N1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 36, 23, 36, 11, 5, 1, 1, 1, 1, 1, 1, 1, 11, 17, 17, 17, 56, 57, 109, 109, 109, 109, 109, 43, 43, 43, 43, 43, 43, 43, 43, 43, 23, 11, 5, 5, 1, 1, 1, 17, 56, 56, 57, 57] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47]) total number of confs: 416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581389 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581389 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581389/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581389 Building REAL300025581390 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581390' /scratch/stefan/7787361/working/building/REAL300025581390 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581390 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581390/0 /scratch/stefan/7787361/working/building/REAL300025581390 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/912 `/scratch/stefan/7787361/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CC2=CC=CC=C2O[C@H]1C(F)(F)F) `REAL300025581390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581390 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CC2=CC=CC=C2O[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 28, 45, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 28, 28, 45, 45, 1, 1, 1, 1, 1, 1] 101 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 279 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581390 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CC2=CC=CC=C2O[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 22, 8, 1, 1, 1, 1, 1, 1, 1, 77, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 77, 23, 23, 8, 8, 101, 101, 101, 101, 101, 101] 101 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 335 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581390 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581390 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581390/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581390 Building REAL300025581391 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581391' /scratch/stefan/7787361/working/building/REAL300025581391 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581391 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581391/0 /scratch/stefan/7787361/working/building/REAL300025581391 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/913 `/scratch/stefan/7787361/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)(F)F)SC=C1) `REAL300025581391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581391 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)(F)F)SC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [7, 1, 7, 7, 37, 59, 133, 133, 133, 133, 133, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 37, 37, 59, 59, 1, 1] 133 rigid atoms, others: [1, 11, 12, 13, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 20, 21, 22, 23, 24]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581391 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)(F)F)SC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [82, 82, 22, 8, 1, 1, 1, 1, 1, 1, 1, 81, 133, 133, 133, 133, 133, 133, 133, 133, 81, 22, 22, 8, 8, 133, 133] 133 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581391 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581391 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581391/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581391 Building REAL300025581392 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581392' /scratch/stefan/7787361/working/building/REAL300025581392 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581392 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581392/0 /scratch/stefan/7787361/working/building/REAL300025581392 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/914 `/scratch/stefan/7787361/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2CCOCC2)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025581392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581392 none CC1=NN(C2CCOCC2)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 166, 166, 201, 201, 201, 201, 201, 82, 82, 82, 22, 8, 1, 1, 1, 1, 1, 1, 1, 166, 166, 166, 166, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 22, 22, 8, 8, 166] 201 rigid atoms, others: [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: 519 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581392 none CC1=NN(C2CCOCC2)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 85, 99, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 85, 85, 99, 99, 6] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40]) total number of confs: 537 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581392 none CC1=NN(C2CCOCC2)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 10, 10, 10, 49, 65, 166, 166, 166, 166, 166, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 49, 49, 65, 65, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 40, 10, 11, 22] set([5, 6, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581392 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581392 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581392/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581392 Building REAL300025581393 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581393' /scratch/stefan/7787361/working/building/REAL300025581393 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581393 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581393/0 /scratch/stefan/7787361/working/building/REAL300025581393 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/915 `/scratch/stefan/7787361/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(NC(=O)OCC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581393 none CC(C)(C)C(NC(=O)OCC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 22, 37, 62, 94, 94, 94, 201, 201, 201, 201, 201, 201, 22, 22, 12, 7, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 62, 201, 201, 201, 201, 201, 201, 201, 22, 12, 12, 7, 7] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 859 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581393 none CC(C)(C)C(NC(=O)OCC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 25, 16, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 43, 58, 58, 58, 126, 127, 201, 201, 201, 201, 201, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 25, 3, 3, 1, 1, 1, 1, 1, 58, 126, 126, 127, 127] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581393 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581393 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581393/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581393 Building REAL300025581394 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581394' /scratch/stefan/7787361/working/building/REAL300025581394 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581394 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581394/0 /scratch/stefan/7787361/working/building/REAL300025581394 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/916 `/scratch/stefan/7787361/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)NC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581394 none CC(=O)NC(C)(C)C(=O)NC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 171, 117, 171, 171, 117, 117, 113, 63, 113, 113, 63, 63, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 171, 171, 171, 171, 171, 171, 117, 113, 113, 113, 113, 113, 113, 62, 23, 22, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 879 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581394 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581394 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581394/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581394 Building REAL300025581395 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581395' /scratch/stefan/7787361/working/building/REAL300025581395 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581395 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581395/0 /scratch/stefan/7787361/working/building/REAL300025581395 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/917 `/scratch/stefan/7787361/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)N(C(=O)OCC2=CC=CC=C2)C1) `REAL300025581395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581395 none CO[C@@H]1C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)N(C(=O)OCC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 31, 31, 31, 31, 31, 31, 31, 49, 49, 49, 98, 101, 201, 201, 201, 201, 201, 23, 17, 23, 3, 1, 1, 1, 1, 1, 1, 1, 31, 66, 66, 66, 31, 31, 49, 98, 98, 101, 101, 3, 3, 1, 1, 1, 1, 1, 31, 31] 201 rigid atoms, others: [42, 43, 44, 45, 46, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 599 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581395 none CO[C@@H]1C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)N(C(=O)OCC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 38, 38, 38, 38, 32, 38, 32, 32, 12, 7, 1, 1, 1, 1, 1, 1, 1, 38, 38, 53, 53, 59, 151, 201, 201, 151, 201, 201, 38, 57, 57, 57, 38, 38, 32, 12, 12, 7, 7, 151, 151, 201, 201, 158, 201, 201, 38, 38] 201 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 864 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581395 none CO[C@@H]1C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)N(C(=O)OCC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 16, 38, 38, 38, 38, 38, 1, 1, 2, 2, 4, 20, 31, 31, 20, 31, 31, 1, 5, 5, 5, 1, 1, 5, 13, 13, 16, 16, 20, 20, 31, 31, 21, 31, 31, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 7, 34, 47, 48, 18, 19, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581395 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581395 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581395/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581395 Building REAL300025581396 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581396' /scratch/stefan/7787361/working/building/REAL300025581396 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581396 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581396/0 /scratch/stefan/7787361/working/building/REAL300025581396 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/918 `/scratch/stefan/7787361/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(Cl)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl) `REAL300025581396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581396 none CN1N=C(Cl)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 179, 179, 75, 75, 75, 24, 8, 1, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 179, 75, 24, 24, 8, 8] 179 rigid atoms, others: [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]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581396 none CN1N=C(Cl)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 37, 63, 179, 179, 179, 179, 179, 1, 1, 2, 2, 2, 5, 37, 37, 63, 63] 179 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581396 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581396 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581396/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581396 Building REAL300025581397 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581397' /scratch/stefan/7787361/working/building/REAL300025581397 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581397 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581397/0 /scratch/stefan/7787361/working/building/REAL300025581397 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/919 `/scratch/stefan/7787361/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)(F)F)N(C2=CC=CC=N2)N=C1) `REAL300025581397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581397 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)(F)F)N(C2=CC=CC=N2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [23, 4, 23, 23, 69, 97, 172, 172, 172, 172, 172, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 23, 69, 69, 97, 97, 1, 1, 1, 1, 4] 172 rigid atoms, others: [32, 33, 34, 17, 18, 19, 20, 21, 22, 23, 31] 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, 35]) total number of confs: 522 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581397 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)(F)F)N(C2=CC=CC=N2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [11, 1, 11, 11, 53, 84, 172, 172, 172, 172, 172, 1, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 1, 1, 11, 53, 53, 84, 84, 4, 4, 4, 4, 1] 172 rigid atoms, others: [1, 35, 11, 12, 13, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 497 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581397 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)(F)F)N(C2=CC=CC=N2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [92, 92, 23, 8, 1, 1, 1, 1, 1, 1, 1, 92, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 92, 23, 23, 8, 8, 172, 172, 172, 172, 172] 172 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581397 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581397 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581397/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581397 Building REAL300025581398 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581398' /scratch/stefan/7787361/working/building/REAL300025581398 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581398 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581398/0 /scratch/stefan/7787361/working/building/REAL300025581398 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/920 `/scratch/stefan/7787361/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCC1CC1=CC=CC=C1) `REAL300025581398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581398 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 24, 24, 88, 98, 201, 201, 201, 201, 201, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 24, 88, 88, 98, 98, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 539 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: REAL300025581398 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 53, 65, 167, 167, 167, 167, 167, 1, 1, 1, 1, 1, 1, 5, 6, 6, 5, 6, 6, 10, 53, 53, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 5, 6, 6] 201 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 413 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581398 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 8, 1, 1, 1, 1, 1, 1, 1, 72, 167, 167, 167, 167, 167, 201, 201, 201, 201, 201, 201, 72, 21, 20, 8, 8, 167, 167, 167, 167, 167, 167, 167, 167, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 680 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581398 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581398 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581398/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581398 Building REAL300025581399 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581399' /scratch/stefan/7787361/working/building/REAL300025581399 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581399 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581399/0 /scratch/stefan/7787361/working/building/REAL300025581399 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/921 `/scratch/stefan/7787361/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1CCC1=CC=CC=C1) `REAL300025581399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581399 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1CCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 22, 22, 92, 108, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 92, 92, 108, 108, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 559 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581399 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1CCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 32, 44, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 8, 32, 32, 44, 44, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581399 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1CCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 23, 8, 1, 1, 1, 1, 1, 1, 1, 77, 137, 137, 137, 137, 137, 199, 199, 201, 201, 201, 201, 201, 77, 23, 23, 8, 8, 137, 137, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 689 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581399 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581399 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581399/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581399 Building REAL300025581400 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581400' /scratch/stefan/7787361/working/building/REAL300025581400 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581400 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581400/0 /scratch/stefan/7787361/working/building/REAL300025581400 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/922 `/scratch/stefan/7787361/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CN(CC(=O)NCCC2=NC(=O)O[N-]2)C(=O)[N-]C1=O) `REAL300025581400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581400 none N#CC1=CN(CC(=O)NCCC2=NC(=O)O[N-]2)C(=O)[N-]C1=O NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 3, 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, 98, 95, 54, 54, 55, 13, 8, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 98, 95, 95, 54, 13, 13, 8, 8] 98 rigid atoms, others: [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]) total number of confs: 373 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581400 none N#CC1=CN(CC(=O)NCCC2=NC(=O)O[N-]2)C(=O)[N-]C1=O NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 50, 58, 98, 98, 98, 98, 98, 1, 1, 1, 1, 1, 1, 4, 4, 15, 50, 50, 58, 58] 98 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581400 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581400 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581400/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581400 Building REAL300025581401 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581401' /scratch/stefan/7787361/working/building/REAL300025581401 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581401 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581401/0 /scratch/stefan/7787361/working/building/REAL300025581401 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/923 `/scratch/stefan/7787361/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)N(C(=O)OCC2=CC=CC=C2)C1) `REAL300025581401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581401 none CO[C@@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)N(C(=O)OCC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 51, 51, 51, 51, 51, 51, 51, 54, 54, 54, 108, 108, 201, 201, 201, 201, 201, 34, 21, 34, 4, 1, 1, 1, 1, 1, 1, 1, 51, 67, 67, 67, 51, 51, 54, 108, 108, 108, 108, 4, 4, 1, 1, 1, 1, 1, 51, 51] 201 rigid atoms, others: [42, 43, 44, 45, 46, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 581 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581401 none CO[C@@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)N(C(=O)OCC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 21, 21, 21, 21, 19, 21, 19, 19, 11, 8, 1, 1, 1, 1, 1, 1, 1, 21, 21, 34, 34, 51, 178, 201, 201, 201, 201, 201, 21, 36, 36, 36, 21, 21, 19, 11, 11, 8, 8, 178, 178, 201, 201, 201, 201, 201, 21, 21] 201 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 714 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581401 none CO[C@@H]1C[C@@H](C(=O)NCCC2=NC(=O)O[N-]2)N(C(=O)OCC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 21, 21, 21, 21, 21, 1, 1, 3, 3, 7, 29, 51, 51, 51, 51, 51, 1, 5, 5, 5, 1, 1, 4, 8, 8, 8, 8, 29, 29, 51, 51, 51, 51, 51, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 7, 34, 47, 48, 18, 19, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581401 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581401 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581401/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581401 Building REAL300025581402 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581402' /scratch/stefan/7787361/working/building/REAL300025581402 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581402 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581402/0 /scratch/stefan/7787361/working/building/REAL300025581402 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/924 `/scratch/stefan/7787361/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2CCCC2)CCNC1=O) `REAL300025581402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581402 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2CCCC2)CCNC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 16, 71, 95, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 16, 71, 71, 95, 95, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 27, 28, 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, 36, 37, 38, 39, 40]) total number of confs: 572 number of broken/clashed sets: 93 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581402 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2CCCC2)CCNC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 30, 47, 131, 131, 131, 131, 131, 1, 1, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6, 30, 30, 47, 47, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 36, 37, 38, 39, 40, 11, 12, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 334 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581402 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2CCCC2)CCNC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 21, 8, 1, 1, 1, 1, 1, 1, 1, 75, 131, 201, 201, 201, 201, 131, 131, 131, 131, 131, 75, 21, 21, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 131, 131, 131, 131] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 652 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581402 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581402 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581402/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581402 Building REAL300025581403 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581403' /scratch/stefan/7787361/working/building/REAL300025581403 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581403 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581403/0 /scratch/stefan/7787361/working/building/REAL300025581403 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/925 `/scratch/stefan/7787361/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC1(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL300025581403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581403 none CC1(C)CC1(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 1, 4, 15, 15, 15, 55, 75, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 15, 55, 55, 75, 75, 1, 1, 1, 1, 1] 148 rigid atoms, others: [35, 4, 37, 38, 39, 16, 17, 18, 19, 20, 21, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 429 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581403 none CC1(C)CC1(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 138, 81, 81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 138, 148, 148, 148, 148, 148, 138, 138, 138, 138, 138, 138, 138, 138, 80, 25, 25, 8, 8, 148, 148, 148, 148, 148] 148 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 464 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581403 none CC1(C)CC1(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 37, 60, 138, 138, 138, 138, 138, 1, 4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1, 8, 37, 37, 60, 60, 4, 4, 3, 4, 4] 148 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 397 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581403 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581403 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581403/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581403 Building REAL300025581404 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581404' /scratch/stefan/7787361/working/building/REAL300025581404 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581404 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581404/0 /scratch/stefan/7787361/working/building/REAL300025581404 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/926 `/scratch/stefan/7787361/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC=C1C(F)(F)F) `REAL300025581404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581404 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [7, 1, 7, 7, 47, 67, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 47, 47, 67, 67, 1, 1] 147 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 393 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581404 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [89, 89, 22, 8, 1, 1, 1, 1, 1, 1, 1, 89, 147, 147, 147, 147, 147, 147, 147, 147, 88, 22, 22, 8, 8, 147, 147] 147 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581404 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581404 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581404/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581404 Building REAL300025581405 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581405' /scratch/stefan/7787361/working/building/REAL300025581405 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581405 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581405/0 /scratch/stefan/7787361/working/building/REAL300025581405 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/927 `/scratch/stefan/7787361/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1) `REAL300025581405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581405 none CCCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 4, 1, 4, 12, 12, 12, 58, 67, 171, 171, 171, 171, 171, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 9, 9, 4, 12, 58, 58, 67, 67, 1, 1, 1, 1] 201 rigid atoms, others: [19, 3, 36, 37, 38, 15, 16, 17, 18, 35, 20, 21] set([0, 1, 2, 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: 442 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581405 none CCCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 144, 65, 65, 65, 19, 8, 1, 1, 1, 1, 1, 1, 1, 144, 171, 171, 171, 171, 171, 171, 183, 183, 183, 183, 183, 183, 183, 144, 65, 19, 19, 8, 8, 171, 171, 171, 171] 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, 34, 35, 36, 37, 38]) total number of confs: 816 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581405 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581405 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581405/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581405 Building REAL300025581406 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581406' /scratch/stefan/7787361/working/building/REAL300025581406 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581406 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581406/0 /scratch/stefan/7787361/working/building/REAL300025581406 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/928 `/scratch/stefan/7787361/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2CCOCC2)C(C)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581406 none CC1=NN(C2CCOCC2)C(C)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 187, 187, 201, 201, 201, 201, 201, 187, 187, 72, 72, 72, 21, 8, 1, 1, 1, 1, 1, 1, 1, 187, 187, 187, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 187, 187, 72, 21, 21, 8, 8] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 444 number of broken/clashed sets: 36 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581406 none CC1=NN(C2CCOCC2)C(C)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 4, 3, 3, 22, 22, 22, 78, 90, 201, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 22, 78, 78, 90, 90] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 27, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 530 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581406 none CC1=NN(C2CCOCC2)C(C)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 9, 9, 9, 45, 61, 187, 187, 187, 187, 187, 2, 2, 2, 3, 3, 3, 3, 4, 3, 4, 3, 3, 2, 2, 2, 9, 45, 45, 61, 61] 201 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 433 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581406 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581406 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581406/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581406 Building REAL300025581407 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581407' /scratch/stefan/7787361/working/building/REAL300025581407 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581407 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581407/0 /scratch/stefan/7787361/working/building/REAL300025581407 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/929 `/scratch/stefan/7787361/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(Br)C(O)=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581407 none O=C(CC1=CC=C(Br)C(O)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 17, 1, 12, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 117, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 402, 201, 53, 17, 17, 8, 8] 402 rigid atoms, others: [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]) total number of confs: 1023 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581407 none O=C(CC1=CC=C(Br)C(O)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 17, 1, 12, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 71, 79, 201, 201, 201, 201, 201, 6, 6, 1, 1, 2, 1, 15, 71, 71, 79, 79] 402 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 25] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 26, 27, 28, 29, 30]) total number of confs: 495 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581407 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581407 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581407/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581407 Building REAL300025581408 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581408' /scratch/stefan/7787361/working/building/REAL300025581408 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581408 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581408/0 /scratch/stefan/7787361/working/building/REAL300025581408 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/930 `/scratch/stefan/7787361/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)N1C=C(C2=CC=CC=C2)N=N1) `REAL300025581408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581408 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)N1C=C(C2=CC=CC=C2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 67, 67, 116, 116, 201, 201, 201, 201, 201, 6, 29, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 67, 116, 116, 116, 116, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 20, 21, 22, 31] 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]) total number of confs: 581 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581408 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)N1C=C(C2=CC=CC=C2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 38, 38, 89, 89, 201, 201, 201, 201, 201, 1, 12, 12, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 38, 89, 89, 89, 89, 1, 6, 6, 5, 6, 6] 201 rigid atoms, others: [11, 14, 15, 16, 17, 23, 24, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 525 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581408 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)N1C=C(C2=CC=CC=C2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 44, 110, 110, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 44, 17, 17, 8, 8, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 581 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581408 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581408 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581408/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581408 Building REAL300025581409 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581409' /scratch/stefan/7787361/working/building/REAL300025581409 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581409 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581409/0 /scratch/stefan/7787361/working/building/REAL300025581409 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/931 `/scratch/stefan/7787361/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C(OC)C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025581409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581409 none COC1=CC=CC(C(OC)C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 199, 199, 199, 199, 87, 45, 87, 93, 45, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 199, 199, 199, 87, 93, 93, 93, 44, 8, 8, 8, 8, 199] 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]) total number of confs: 493 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581409 none COC1=CC=CC(C(OC)C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 12, 19, 12, 26, 26, 26, 88, 88, 199, 199, 198, 199, 199, 1, 3, 3, 3, 1, 1, 1, 12, 19, 19, 19, 26, 88, 88, 88, 88, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 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 /scratch/stefan/7787361/working/building/REAL300025581409 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581409 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581409/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581409 Building REAL300025581410 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581410' /scratch/stefan/7787361/working/building/REAL300025581410 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581410 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581410/0 /scratch/stefan/7787361/working/building/REAL300025581410 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/932 `/scratch/stefan/7787361/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCOCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581410 none COCCOCCOCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 197, 139, 98, 98, 95, 91, 87, 75, 19, 19, 19, 7, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 98, 98, 98, 98, 91, 91, 87, 87, 75, 75, 19, 7, 7, 5, 5] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 781 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581410 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581410 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581410/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581410 Building REAL300025581411 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581411' /scratch/stefan/7787361/working/building/REAL300025581411 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581411 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581411/0 /scratch/stefan/7787361/working/building/REAL300025581411 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/933 `/scratch/stefan/7787361/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2C=C1OC) `REAL300025581411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581411 none COC1=CC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 140, 140, 140, 140, 140, 140, 49, 49, 49, 19, 8, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 201, 201, 201, 201, 140, 140, 140, 49, 19, 19, 8, 8, 140, 140, 201, 201, 201] 201 rigid atoms, others: [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, 39, 40]) total number of confs: 546 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581411 none COC1=CC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 37, 140, 140, 140, 140, 140, 1, 1, 1, 1, 1, 3, 4, 4, 4, 1, 1, 1, 5, 29, 29, 37, 37, 1, 1, 3, 3, 3] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 36, 28, 29, 30, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581411 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581411 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581411/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581411 Building REAL300025581412 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581412' /scratch/stefan/7787361/working/building/REAL300025581412 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581412 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581412/0 /scratch/stefan/7787361/working/building/REAL300025581412 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/934 `/scratch/stefan/7787361/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1(N2C=NN=N2)CCOCC1)NCCC1=NC(=O)O[N-]1) `REAL300025581412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581412 none O=C(CC1(N2C=NN=N2)CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 8, 8, 8, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [61, 61, 61, 105, 123, 172, 172, 172, 172, 123, 123, 123, 123, 123, 17, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 172, 123, 123, 123, 123, 123, 123, 123, 123, 61, 17, 17, 8, 8] 172 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 560 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581412 none O=C(CC1(N2C=NN=N2)CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 8, 8, 8, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [35, 17, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 35, 35, 89, 91, 172, 172, 172, 172, 172, 17, 17, 1, 5, 5, 5, 5, 5, 5, 5, 5, 35, 89, 89, 91, 91] 172 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 522 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581412 none O=C(CC1(N2C=NN=N2)CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 8, 8, 8, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [17, 7, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 17, 50, 52, 123, 123, 123, 123, 123, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 50, 50, 52, 52] 172 rigid atoms, others: [32, 33, 2, 3, 4, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581412 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581412 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581412/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581412 Building REAL300025581413 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581413' /scratch/stefan/7787361/working/building/REAL300025581413 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581413 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581413/0 /scratch/stefan/7787361/working/building/REAL300025581413 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/935 `/scratch/stefan/7787361/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(CC(=O)NCCC1=NC(=O)O[N-]1)C(=O)OC(C)(C)C) `REAL300025581413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581413 none C#CCN(CC(=O)NCCC1=NC(=O)O[N-]1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 126, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 163, 201, 201, 201, 201, 201, 201, 163, 163, 163, 126, 126, 49, 17, 17, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581413 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581413 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581413/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581413 Building REAL300025581414 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581414' /scratch/stefan/7787361/working/building/REAL300025581414 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581414 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581414/0 /scratch/stefan/7787361/working/building/REAL300025581414 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/936 `/scratch/stefan/7787361/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NC=CN=C1SCC1=CC=CC=C1) `REAL300025581414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581414 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC=CN=C1SCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 8, 1, 14, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 28, 64, 63, 119, 119, 201, 201, 201, 201, 201, 28, 28, 28, 28, 28, 7, 3, 1, 1, 1, 1, 1, 1, 1, 64, 119, 119, 119, 119, 28, 28, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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]) total number of confs: 590 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581414 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC=CN=C1SCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 8, 1, 14, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 33, 37, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1, 1, 7, 28, 28, 28, 28, 28, 28, 7, 33, 33, 37, 37, 1, 1, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 321 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581414 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC=CN=C1SCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 8, 1, 14, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 15, 7, 1, 1, 1, 1, 1, 1, 1, 43, 102, 102, 102, 102, 102, 102, 175, 201, 201, 201, 201, 201, 201, 43, 15, 15, 7, 7, 102, 102, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 499 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581414 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581414 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581414/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581414 Building REAL300025581415 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581415' /scratch/stefan/7787361/working/building/REAL300025581415 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581415 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581415/0 /scratch/stefan/7787361/working/building/REAL300025581415 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/937 `/scratch/stefan/7787361/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2CCOCC2)=N1) `REAL300025581415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581415 none CCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 6, 6, 6, 6, 6, 15, 15, 15, 65, 65, 136, 136, 136, 136, 136, 1, 1, 1, 1, 1, 1, 1, 6, 26, 26, 26, 26, 26, 6, 15, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 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]) total number of confs: 406 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581415 none CCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 105, 105, 105, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 136, 136, 136, 136, 136, 105, 167, 167, 167, 167, 167, 105, 49, 17, 17, 8, 8, 136, 136, 136, 136, 136, 136, 136, 136, 136] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 745 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581415 none CCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 6, 6, 6, 30, 33, 105, 105, 105, 105, 105, 1, 1, 6, 6, 6, 6, 6, 1, 8, 8, 8, 8, 8, 1, 6, 30, 30, 33, 33, 6, 6, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 23, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581415 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581415 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581415/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581415 Building REAL300025581416 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581416' /scratch/stefan/7787361/working/building/REAL300025581416 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581416 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581416/0 /scratch/stefan/7787361/working/building/REAL300025581416 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/938 `/scratch/stefan/7787361/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC=C2OC1C(F)(F)F) `REAL300025581416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581416 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC=C2OC1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 66, 96, 177, 177, 177, 177, 177, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 66, 66, 96, 96, 1, 1, 1, 1, 1, 1] 177 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29]) total number of confs: 534 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581416 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC=C2OC1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 76, 177, 177, 177, 177, 177, 177, 177, 177, 177, 177, 177, 177, 177, 75, 24, 24, 8, 8, 177, 177, 177, 177, 177, 177] 177 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581416 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581416 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581416/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581416 Building REAL300025581417 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581417' /scratch/stefan/7787361/working/building/REAL300025581417 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581417 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581417/0 /scratch/stefan/7787361/working/building/REAL300025581417 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/939 `/scratch/stefan/7787361/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NC1=CC=CN=C1Cl)C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581417 none CCC(NC1=CC=CN=C1Cl)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 16, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 127, 46, 127, 186, 197, 197, 197, 197, 197, 197, 46, 46, 15, 7, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 171, 127, 186, 197, 197, 197, 46, 15, 15, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 1003 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581417 none CCC(NC1=CC=CN=C1Cl)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 16, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 35, 35, 35, 100, 101, 197, 197, 197, 197, 197, 20, 20, 20, 20, 20, 12, 4, 1, 1, 1, 35, 100, 100, 101, 101] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 601 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581417 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581417 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581417/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581417 Building REAL300025581418 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581418' /scratch/stefan/7787361/working/building/REAL300025581418 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581418 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581418/0 /scratch/stefan/7787361/working/building/REAL300025581418 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/940 `/scratch/stefan/7787361/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CS(=O)(=O)CC1C(F)(F)F) `REAL300025581418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581418 none O=C(NCCC1=NC(=O)O[N-]1)C1CS(=O)(=O)CC1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 14, 11, 11, 5, 5, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 17, 29, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 17, 17, 29, 29, 1, 1, 1, 1, 1, 1] 58 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581418 none O=C(NCCC1=NC(=O)O[N-]1)C1CS(=O)(=O)CC1C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 14, 11, 11, 5, 5, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 20, 8, 1, 1, 1, 1, 1, 1, 1, 52, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 52, 21, 21, 8, 8, 58, 58, 58, 58, 58, 58] 58 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581418 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581418 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581418/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581418 Building REAL300025581419 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581419' /scratch/stefan/7787361/working/building/REAL300025581419 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581419 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581419/0 /scratch/stefan/7787361/working/building/REAL300025581419 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/941 `/scratch/stefan/7787361/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2CCOCC2)=N1) `REAL300025581419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581419 none CC(C)N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 35, 6, 6, 6, 6, 15, 15, 15, 70, 72, 186, 186, 186, 186, 186, 1, 1, 1, 1, 1, 1, 1, 6, 35, 35, 35, 35, 35, 35, 35, 6, 15, 70, 70, 72, 72, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 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]) total number of confs: 518 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581419 none CC(C)N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 124, 158, 116, 124, 49, 49, 49, 19, 8, 1, 1, 1, 1, 1, 1, 1, 124, 124, 186, 186, 186, 186, 186, 124, 158, 158, 158, 158, 158, 158, 158, 124, 49, 19, 19, 8, 8, 186, 186, 186, 186, 186, 186, 186, 186, 186] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581419 none CC(C)N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 1, 1, 1, 1, 5, 5, 5, 29, 33, 124, 124, 124, 124, 124, 1, 1, 6, 6, 6, 6, 6, 1, 11, 11, 11, 11, 11, 11, 11, 1, 5, 29, 29, 33, 34, 6, 6, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 17, 18, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581419 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581419 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581419/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581419 Building REAL300025581420 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581420' /scratch/stefan/7787361/working/building/REAL300025581420 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581420 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581420/0 /scratch/stefan/7787361/working/building/REAL300025581420 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/942 `/scratch/stefan/7787361/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CCO)N=C1C1CCOCC1) `REAL300025581420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581420 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CCO)N=C1C1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 12, 8, 1, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 16, 58, 59, 140, 140, 140, 140, 140, 6, 6, 6, 6, 28, 32, 6, 1, 1, 1, 1, 1, 1, 1, 16, 58, 58, 59, 59, 6, 28, 28, 32, 32, 96, 1, 1, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 526 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581420 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CCO)N=C1C1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 12, 8, 1, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 27, 29, 100, 100, 100, 100, 100, 1, 1, 1, 1, 8, 10, 1, 1, 1, 6, 6, 6, 6, 6, 5, 27, 27, 29, 29, 1, 8, 8, 10, 10, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6] 603 rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 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: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581420 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CCO)N=C1C1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 12, 8, 1, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 17, 8, 1, 1, 1, 1, 1, 1, 1, 44, 100, 96, 100, 161, 161, 100, 100, 100, 140, 140, 140, 140, 140, 44, 17, 17, 8, 8, 100, 161, 161, 161, 161, 483, 140, 140, 140, 140, 140, 140, 140, 140, 140] 603 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 1239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581420 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581420 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581420/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581420 Building REAL300025581421 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581421' /scratch/stefan/7787361/working/building/REAL300025581421 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581421 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581421/0 /scratch/stefan/7787361/working/building/REAL300025581421 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/943 `/scratch/stefan/7787361/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(CN2C=NC=N2)=C1) `REAL300025581421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581421 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(CN2C=NC=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 15, 41, 41, 112, 114, 201, 201, 201, 201, 201, 15, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 15, 41, 112, 112, 114, 114, 15, 15, 15, 8, 8, 1, 1, 15] 201 rigid atoms, others: [33, 34, 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, 35]) total number of confs: 591 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581421 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(CN2C=NC=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 23, 27, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 1, 5, 23, 23, 27, 27, 1, 1, 1, 4, 4, 15, 15, 1] 201 rigid atoms, others: [1, 35, 11, 12, 13, 14, 15, 16, 22, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581421 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(CN2C=NC=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 15, 7, 1, 1, 1, 1, 1, 1, 1, 36, 78, 78, 50, 78, 78, 163, 201, 201, 201, 201, 78, 36, 15, 15, 7, 7, 78, 78, 78, 163, 163, 201, 201, 78] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 795 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581421 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581421 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581421/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581421 Building REAL300025581422 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581422' /scratch/stefan/7787361/working/building/REAL300025581422 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581422 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581422/0 /scratch/stefan/7787361/working/building/REAL300025581422 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/944 `/scratch/stefan/7787361/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(O)=C(O)C=C2S1) `REAL300025581422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581422 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(O)=C(O)C=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 12, 1, 12, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 32, 35, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 31, 35, 35, 1, 1, 2, 2, 1] 268 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 183 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581422 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(O)=C(O)C=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 12, 1, 12, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 20, 8, 1, 1, 1, 1, 1, 1, 1, 49, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 48, 20, 20, 8, 8, 67, 67, 134, 134, 67] 268 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 473 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581422 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581422 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581422/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581422 Building REAL300025581423 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581423' /scratch/stefan/7787361/working/building/REAL300025581423 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581423 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581423/0 /scratch/stefan/7787361/working/building/REAL300025581423 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/945 `/scratch/stefan/7787361/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1I) `REAL300025581423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581423 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1I NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 18, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 37, 66, 177, 177, 177, 177, 177, 1, 1, 1, 1, 1, 1, 7, 37, 37, 66, 66, 1, 1] 177 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) total number of confs: 446 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581423 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1I NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 18, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 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: [111, 111, 24, 8, 1, 1, 1, 1, 1, 1, 1, 111, 177, 177, 177, 177, 177, 111, 24, 24, 8, 8, 177, 177] 177 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581423 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581423 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581423/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581423 Building REAL300025581424 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581424' /scratch/stefan/7787361/working/building/REAL300025581424 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581424 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581424/0 /scratch/stefan/7787361/working/building/REAL300025581424 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/946 `/scratch/stefan/7787361/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=CN=C2C(Br)=C1) `REAL300025581424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581424 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=CN=C2C(Br)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 8, 1, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 7, 7, 49, 71, 157, 157, 157, 157, 157, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 49, 49, 71, 71, 1, 1, 1, 1] 157 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581424 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=CN=C2C(Br)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 8, 1, 1, 17, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 20, 8, 1, 1, 1, 1, 1, 1, 1, 71, 157, 157, 157, 157, 157, 157, 157, 157, 157, 70, 20, 20, 8, 8, 157, 157, 157, 157] 157 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 353 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581424 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581424 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581424/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581424 Building REAL300025581425 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581425' /scratch/stefan/7787361/working/building/REAL300025581425 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581425 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581425/0 /scratch/stefan/7787361/working/building/REAL300025581425 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/947 `/scratch/stefan/7787361/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(C1)CC(C(=O)NCCC1=NC(=O)O[N-]1)=NO2) `REAL300025581425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581425 none CC(C)(C)OC(=O)N1CC2(C1)CC(C(=O)NCCC1=NC(=O)O[N-]1)=NO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 153, 93, 153, 93, 93, 93, 93, 93, 45, 45, 45, 18, 8, 1, 1, 1, 1, 1, 1, 1, 92, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 93, 93, 93, 44, 18, 18, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 551 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581425 none CC(C)(C)OC(=O)N1CC2(C1)CC(C(=O)NCCC1=NC(=O)O[N-]1)=NO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 43, 45, 92, 92, 92, 92, 92, 1, 1, 6, 6, 6, 5, 5, 5, 6, 6, 6, 1, 1, 1, 1, 1, 1, 12, 43, 43, 45, 45] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 24, 25, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581425 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581425 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581425/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581425 Building REAL300025581426 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581426' /scratch/stefan/7787361/working/building/REAL300025581426 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581426 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581426/0 /scratch/stefan/7787361/working/building/REAL300025581426 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/948 `/scratch/stefan/7787361/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(I)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581426 none CN1N=C(I)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'I', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 18, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 146, 146, 82, 82, 82, 24, 8, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 82, 24, 24, 8, 8] 146 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]) total number of confs: 367 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581426 none CN1N=C(I)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'I', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 18, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 61, 83, 146, 146, 146, 146, 146, 2, 2, 2, 1, 13, 61, 61, 83, 83] 146 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 438 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581426 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581426 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581426/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581426 Building REAL300025581427 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581427' /scratch/stefan/7787361/working/building/REAL300025581427 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581427 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581427/0 /scratch/stefan/7787361/working/building/REAL300025581427 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/949 `/scratch/stefan/7787361/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025581427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581427 none CC(C)(C)OC(=O)N[C@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 187, 151, 187, 88, 88, 88, 88, 88, 41, 88, 41, 41, 15, 8, 1, 1, 1, 1, 1, 1, 1, 88, 88, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 88, 88, 88, 88, 41, 15, 15, 8, 8, 88, 88, 88, 88] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581427 none CC(C)(C)OC(=O)N[C@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 6, 4, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 29, 29, 88, 88, 88, 88, 88, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 7, 29, 29, 29, 29, 1, 1, 1, 1] 201 rigid atoms, others: [49, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 46, 25, 39, 26] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581427 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581427 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581427/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581427 Building REAL300025581428 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581428' /scratch/stefan/7787361/working/building/REAL300025581428 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581428 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581428/0 /scratch/stefan/7787361/working/building/REAL300025581428 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/950 `/scratch/stefan/7787361/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(OC2=CC=C(Cl)C=N2)=C1) `REAL300025581428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581428 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(OC2=CC=C(Cl)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 25, 51, 51, 121, 122, 201, 201, 201, 201, 201, 25, 25, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 25, 51, 121, 121, 122, 122, 25, 25, 25, 1, 1, 1, 25] 201 rigid atoms, others: [33, 34, 35, 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, 36]) total number of confs: 604 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581428 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(OC2=CC=C(Cl)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 21, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 25, 25, 1, 5, 19, 19, 21, 21, 1, 1, 1, 25, 25, 25, 1] 201 rigid atoms, others: [32, 1, 36, 11, 12, 13, 14, 15, 16, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581428 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(OC2=CC=C(Cl)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 5, 1, 1, 1, 1, 1, 1, 1, 17, 43, 43, 43, 43, 43, 155, 201, 201, 201, 201, 201, 201, 43, 17, 7, 7, 5, 5, 43, 43, 43, 201, 201, 201, 43] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581428 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581428 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581428/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581428 Building REAL300025581429 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581429' /scratch/stefan/7787361/working/building/REAL300025581429 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581429 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581429/0 /scratch/stefan/7787361/working/building/REAL300025581429 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/951 `/scratch/stefan/7787361/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)F)N=C2CCCCN21) `REAL300025581429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581429 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)F)N=C2CCCCN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 8, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 43, 65, 193, 193, 193, 193, 193, 1, 1, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 10, 43, 43, 65, 65, 9, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 33, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 23, 24, 25, 26, 27, 28]) total number of confs: 480 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581429 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C(F)F)N=C2CCCCN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 8, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 90, 193, 193, 201, 201, 193, 193, 193, 193, 193, 193, 193, 89, 24, 24, 8, 8, 201, 193, 193, 193, 193, 193, 193, 193, 193] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581429 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581429 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581429/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581429 Building REAL300025581430 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581430' /scratch/stefan/7787361/working/building/REAL300025581430 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581430 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581430/0 /scratch/stefan/7787361/working/building/REAL300025581430 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/952 `/scratch/stefan/7787361/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(Cl)N=CC=C2O1) `REAL300025581430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581430 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(Cl)N=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [12, 1, 12, 13, 60, 76, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 60, 60, 76, 76, 1, 1, 1] 134 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 392 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581430 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(Cl)N=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [79, 79, 20, 8, 1, 1, 1, 1, 1, 1, 1, 79, 134, 134, 134, 134, 134, 134, 134, 134, 132, 79, 20, 20, 8, 8, 134, 134, 134] 134 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581430 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581430 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581430/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581430 Building REAL300025581431 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581431' /scratch/stefan/7787361/working/building/REAL300025581431 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581431 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581431/0 /scratch/stefan/7787361/working/building/REAL300025581431 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/953 `/scratch/stefan/7787361/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCNC(=O)C1=CC2=CC=CC=C2N1)NCCC1=NC(=O)O[N-]1) `REAL300025581431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581431 none O=C(CCNC(=O)C1=CC2=CC=CC=C2N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 125, 167, 182, 184, 182, 199, 199, 199, 199, 199, 199, 199, 199, 8, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 169, 169, 184, 199, 199, 199, 199, 199, 199, 38, 9, 9, 8, 8] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 788 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581431 none O=C(CCNC(=O)C1=CC2=CC=CC=C2N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 26, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 110, 110, 199, 199, 199, 199, 199, 26, 26, 18, 18, 4, 1, 1, 1, 1, 1, 1, 68, 113, 113, 113, 113] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581431 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581431 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581431/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581431 Building REAL300025581432 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581432' /scratch/stefan/7787361/working/building/REAL300025581432 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581432 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581432/0 /scratch/stefan/7787361/working/building/REAL300025581432 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/954 `/scratch/stefan/7787361/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C2=CC=CC(Br)=C2)CC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581432 none CC1(C2=CC=CC(Br)=C2)CC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 201, 201, 201, 201, 201, 201, 128, 65, 65, 65, 19, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 201, 201, 201, 201, 128, 128, 128, 65, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 558 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581432 none CC1(C2=CC=CC(Br)=C2)CC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 70, 80, 201, 201, 201, 201, 201, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 15, 70, 70, 80, 80] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 490 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581432 none CC1(C2=CC=CC(Br)=C2)CC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 5, 5, 2, 5, 5, 5, 1, 1, 1, 6, 6, 6, 28, 36, 128, 128, 128, 128, 128, 2, 2, 2, 5, 5, 3, 5, 1, 1, 1, 6, 28, 28, 36, 36] 201 rigid atoms, others: [0, 1, 2, 9, 10, 11, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581432 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581432 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581432/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581432 Building REAL300025581433 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581433' /scratch/stefan/7787361/working/building/REAL300025581433 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581433 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581433/0 /scratch/stefan/7787361/working/building/REAL300025581433 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/955 `/scratch/stefan/7787361/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC2=CC=CC=C2)C=N1) `REAL300025581433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581433 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 6, 32, 32, 101, 118, 201, 201, 201, 201, 201, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 101, 101, 118, 118, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39]) total number of confs: 604 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581433 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 29, 43, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 1, 9, 29, 29, 43, 43, 1, 1, 2, 2, 6, 6, 6, 6, 6, 1] 201 rigid atoms, others: [1, 39, 11, 12, 13, 14, 15, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581433 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(OCC2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 89, 131, 131, 131, 131, 201, 201, 201, 201, 201, 201, 201, 131, 131, 89, 24, 24, 8, 8, 131, 131, 201, 201, 201, 201, 201, 201, 201, 131] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 492 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581433 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581433 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581433/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581433 Building REAL300025581434 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581434' /scratch/stefan/7787361/working/building/REAL300025581434 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581434 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581434/0 /scratch/stefan/7787361/working/building/REAL300025581434 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/956 `/scratch/stefan/7787361/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(OC(C)C(F)(F)F)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581434 none CC1=NC(OC(C)C(F)(F)F)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 136, 160, 201, 201, 201, 201, 201, 136, 136, 51, 51, 51, 17, 8, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 201, 201, 201, 201, 136, 136, 51, 17, 17, 8, 8] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 587 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581434 none CC1=NC(OC(C)C(F)(F)F)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 1, 1, 1, 1, 9, 9, 9, 40, 43, 136, 136, 136, 136, 136, 2, 2, 2, 14, 15, 15, 15, 1, 1, 9, 40, 40, 43, 43] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581434 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581434 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581434/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581434 Building REAL300025581435 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581435' /scratch/stefan/7787361/working/building/REAL300025581435 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581435 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581435/0 /scratch/stefan/7787361/working/building/REAL300025581435 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/957 `/scratch/stefan/7787361/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)=CS1) `REAL300025581435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581435 none CC1=NC(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 152, 152, 152, 152, 73, 73, 73, 23, 8, 1, 1, 1, 1, 1, 1, 1, 152, 201, 201, 201, 201, 201, 152, 152, 73, 23, 23, 8, 8, 201] 201 rigid atoms, others: [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: 442 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581435 none CC1=NC(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 11, 1, 1, 1, 1, 1, 1, 11, 11, 11, 47, 61, 152, 152, 152, 152, 152, 1, 11, 10, 11, 11, 11, 1, 1, 11, 47, 47, 61, 61, 11] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 19, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 394 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581435 none CC1=NC(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 10, 10, 10, 49, 49, 49, 125, 137, 201, 201, 201, 201, 201, 11, 1, 1, 2, 2, 2, 11, 11, 49, 125, 125, 137, 137, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 20, 21] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 626 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581435 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581435 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581435/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581435 Building REAL300025581436 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581436' /scratch/stefan/7787361/working/building/REAL300025581436 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581436 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581436/0 /scratch/stefan/7787361/working/building/REAL300025581436 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/958 `/scratch/stefan/7787361/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CC=C1OCC1=CC=NC=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581436 none O=C(CC1=CC=CC=C1OCC1=CC=NC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 42, 46, 46, 46, 46, 46, 46, 108, 179, 201, 201, 201, 201, 201, 7, 5, 1, 1, 1, 1, 1, 1, 1, 42, 42, 46, 46, 46, 46, 179, 179, 201, 201, 201, 201, 17, 7, 7, 5, 5] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 615 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581436 none O=C(CC1=CC=CC=C1OCC1=CC=NC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 53, 49, 49, 49, 36, 49, 49, 22, 4, 1, 1, 1, 1, 1, 1, 1, 79, 79, 124, 124, 201, 201, 201, 201, 201, 53, 53, 49, 41, 49, 49, 4, 4, 1, 1, 1, 1, 79, 124, 124, 124, 124] 201 rigid atoms, others: [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, 33, 38, 39, 40, 41, 42]) total number of confs: 655 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581436 none O=C(CC1=CC=CC=C1OCC1=CC=NC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 49, 49, 33, 49, 49, 11, 11, 21, 21, 46, 46, 46, 46, 46, 5, 5, 1, 1, 1, 1, 22, 22, 49, 49, 49, 49, 11, 21, 21, 21, 21] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581436 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581436 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581436/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581436 Building REAL300025581437 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581437' /scratch/stefan/7787361/working/building/REAL300025581437 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581437 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581437/0 /scratch/stefan/7787361/working/building/REAL300025581437 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/959 `/scratch/stefan/7787361/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CC[C@H](CC2=CC=CC=C2)O1) `REAL300025581437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581437 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CC[C@H](CC2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 5, 34, 34, 105, 112, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 34, 105, 105, 112, 112, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 15, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 563 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581437 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CC[C@H](CC2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 46, 55, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 46, 46, 55, 55, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 367 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581437 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CC[C@H](CC2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 22, 8, 1, 1, 1, 1, 1, 1, 1, 66, 153, 153, 153, 153, 153, 153, 201, 201, 201, 201, 201, 201, 153, 66, 22, 22, 8, 8, 153, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 756 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581437 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581437 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581437/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581437 Building REAL300025581438 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581438' /scratch/stefan/7787361/working/building/REAL300025581438 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581438 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581438/0 /scratch/stefan/7787361/working/building/REAL300025581438 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/960 `/scratch/stefan/7787361/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1NC(=O)C2=CC=CC=C2NC1=O)NCCC1=NC(=O)O[N-]1) `REAL300025581438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581438 none O=C(C[C@@H]1NC(=O)C2=CC=CC=C2NC1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 160, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 9, 1, 1, 1, 1, 1, 1, 1, 160, 160, 201, 201, 201, 201, 201, 201, 58, 19, 19, 9, 9] 201 rigid atoms, others: [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]) total number of confs: 764 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581438 none O=C(C[C@@H]1NC(=O)C2=CC=CC=C2NC1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 102, 107, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 33, 102, 102, 107, 107] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 34, 35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581438 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581438 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581438/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581438 Building REAL300025581439 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581439' /scratch/stefan/7787361/working/building/REAL300025581439 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581439 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581439/0 /scratch/stefan/7787361/working/building/REAL300025581439 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/961 `/scratch/stefan/7787361/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=NC3=CC=CC=C32)CC1) `REAL300025581439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581439 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=NC3=CC=CC=C32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 5, 27, 27, 101, 105, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 27, 101, 101, 105, 105, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38]) total number of confs: 557 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581439 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=NC3=CC=CC=C32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 59, 65, 144, 144, 144, 144, 144, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 12, 59, 59, 65, 65, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 38, 11, 12, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 371 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581439 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=NC3=CC=CC=C32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 19, 8, 1, 1, 1, 1, 1, 1, 1, 45, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 144, 45, 19, 19, 8, 8, 201, 201, 201, 201, 201, 201, 144, 144, 144, 144] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 524 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581439 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581439 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581439/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581439 Building REAL300025581440 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581440' /scratch/stefan/7787361/working/building/REAL300025581440 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581440 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581440/0 /scratch/stefan/7787361/working/building/REAL300025581440 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/962 `/scratch/stefan/7787361/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=C([N+](=O)[O-])C=C2)CCC1) `REAL300025581440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581440 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=C([N+](=O)[O-])C=C2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 22, 22, 82, 104, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 5, 22, 82, 82, 104, 104, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 568 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581440 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=C([N+](=O)[O-])C=C2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 61, 84, 181, 181, 181, 181, 181, 1, 1, 5, 5, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 61, 61, 84, 84, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 38, 33, 11, 12, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 499 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581440 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=C([N+](=O)[O-])C=C2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 22, 8, 1, 1, 1, 1, 1, 1, 1, 74, 181, 201, 201, 181, 200, 201, 201, 201, 201, 181, 181, 181, 74, 22, 22, 8, 8, 201, 201, 201, 201, 181, 181, 181, 181, 181, 181] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 675 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581440 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581440 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581440/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581440 Building REAL300025581441 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581441' /scratch/stefan/7787361/working/building/REAL300025581441 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581441 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581441/0 /scratch/stefan/7787361/working/building/REAL300025581441 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/963 `/scratch/stefan/7787361/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(F)(F)F)=N1) `REAL300025581441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581441 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 25, 25, 25, 89, 105, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 6, 6, 6, 6, 6, 6, 25, 89, 89, 105, 105, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 14, 15, 16, 17, 18, 19, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581441 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 167, 49, 49, 19, 8, 1, 1, 1, 1, 1, 1, 1, 167, 201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 167, 167, 167, 49, 19, 19, 8, 8, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 706 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581441 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581441 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581441/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581441 Building REAL300025581442 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581442' /scratch/stefan/7787361/working/building/REAL300025581442 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581442 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581442/0 /scratch/stefan/7787361/working/building/REAL300025581442 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/964 `/scratch/stefan/7787361/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1N1N=CC=C1[C@@H]1OCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581442 none COC1=CC=CC=C1N1N=CC=C1[C@@H]1OCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 12, 12, 12, 10, 12, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 31, 76, 76, 76, 76, 76, 17, 17, 17, 12, 12, 12, 12, 5, 5, 1, 1, 1, 1, 6, 28, 28, 31, 31] 201 rigid atoms, others: [40, 41, 42, 43, 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, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 220 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581442 none COC1=CC=CC=C1N1N=CC=C1[C@@H]1OCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 50, 54, 115, 115, 115, 115, 115, 10, 10, 10, 7, 6, 7, 7, 1, 1, 5, 5, 5, 5, 13, 50, 50, 54, 54] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 335 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581442 none COC1=CC=CC=C1N1N=CC=C1[C@@H]1OCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 34, 34, 34, 104, 108, 201, 201, 201, 201, 201, 3, 3, 3, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 34, 104, 104, 108, 108] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 580 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581442 none COC1=CC=CC=C1N1N=CC=C1[C@@H]1OCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 201, 201, 115, 115, 115, 115, 115, 76, 76, 76, 76, 76, 76, 33, 76, 33, 33, 15, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 115, 115, 76, 76, 76, 76, 33, 15, 15, 8, 8] 201 rigid atoms, others: [24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 465 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581442 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581442 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581442/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581442 Building REAL300025581443 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581443' /scratch/stefan/7787361/working/building/REAL300025581443 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581443 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581443/0 /scratch/stefan/7787361/working/building/REAL300025581443 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/965 `/scratch/stefan/7787361/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1) `REAL300025581443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581443 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 14, 46, 49, 107, 107, 107, 107, 107, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 9, 9, 8, 9, 9, 14, 46, 46, 49, 49, 5, 5, 5, 5, 1, 1, 6, 6, 9, 9, 8, 9, 9] 201 rigid atoms, others: [39, 40, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 305 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581443 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 28, 31, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 13, 17, 17, 15, 17, 17, 7, 28, 28, 31, 31, 1, 1, 1, 1, 5, 5, 13, 13, 17, 17, 15, 17, 17] 201 rigid atoms, others: [1, 35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 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, 46, 47]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581443 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 9, 1, 1, 1, 1, 1, 1, 1, 34, 75, 75, 75, 75, 75, 75, 75, 107, 107, 107, 107, 107, 200, 201, 201, 201, 201, 201, 34, 15, 15, 9, 9, 75, 75, 75, 75, 107, 107, 200, 200, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 719 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581443 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 17, 41, 41, 103, 106, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 9, 17, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 41, 103, 103, 106, 106, 17, 17, 17, 17, 9, 9, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 577 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581443 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581443 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581443/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581443 Building REAL300025581444 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581444' /scratch/stefan/7787361/working/building/REAL300025581444 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581444 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581444/0 /scratch/stefan/7787361/working/building/REAL300025581444 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/966 `/scratch/stefan/7787361/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=CC=C1NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581444 none CC(C)C1=CC=CC=C1NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 197, 201, 201, 164, 81, 81, 81, 81, 31, 31, 31, 15, 7, 1, 1, 1, 1, 1, 1, 1, 81, 81, 201, 201, 201, 201, 201, 201, 201, 201, 197, 201, 201, 164, 81, 81, 31, 15, 15, 7, 7, 81, 81] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581444 none CC(C)C1=CC=CC=C1NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 9, 12, 12, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 23, 81, 81, 81, 81, 81, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 9, 12, 12, 6, 1, 1, 5, 23, 23, 23, 23, 1, 1] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 47, 46, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581444 none CC(C)C1=CC=CC=C1NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 7, 7, 35, 35, 35, 110, 110, 201, 201, 201, 201, 201, 12, 12, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 12, 12, 35, 110, 110, 110, 110, 12, 12] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 597 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581444 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581444 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581444/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581444 Building REAL300025581445 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581445' /scratch/stefan/7787361/working/building/REAL300025581445 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581445 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581445/0 /scratch/stefan/7787361/working/building/REAL300025581445 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/967 `/scratch/stefan/7787361/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581445 none COC1=CC=CC=C1NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 197, 201, 201, 197, 63, 36, 102, 102, 36, 36, 36, 15, 7, 1, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 201, 201, 201, 201, 201, 197, 102, 102, 36, 15, 15, 7, 7, 102, 102] 201 rigid atoms, others: [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]) total number of confs: 804 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581445 none COC1=CC=CC=C1NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 8, 8, 6, 8, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 27, 102, 102, 102, 102, 102, 1, 1, 16, 16, 16, 8, 8, 8, 8, 6, 1, 1, 5, 23, 23, 27, 27, 1, 1] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581445 none COC1=CC=CC=C1NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 7, 7, 23, 23, 23, 97, 100, 201, 201, 201, 201, 201, 8, 8, 3, 3, 3, 1, 1, 1, 1, 6, 8, 8, 23, 97, 97, 100, 100, 8, 8] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581445 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581445 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581445/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581445 Building REAL300025581446 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581446' /scratch/stefan/7787361/working/building/REAL300025581446 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581446 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581446/0 /scratch/stefan/7787361/working/building/REAL300025581446 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/968 `/scratch/stefan/7787361/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)C(OC)=C1) `REAL300025581446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581446 none COC1=CC=C(NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 167, 171, 171, 167, 36, 23, 53, 53, 23, 23, 23, 11, 7, 1, 1, 1, 1, 1, 1, 1, 53, 53, 171, 171, 201, 171, 201, 201, 201, 171, 171, 167, 53, 53, 23, 11, 11, 7, 7, 53, 53, 201, 201, 201, 171] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 676 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581446 none COC1=CC=C(NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 6, 8, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 22, 53, 53, 53, 53, 53, 1, 1, 8, 8, 14, 8, 13, 13, 13, 8, 8, 6, 1, 1, 5, 21, 21, 22, 22, 1, 1, 14, 14, 14, 8] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581446 none COC1=CC=C(NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 8, 8, 6, 6, 23, 23, 23, 81, 82, 171, 171, 171, 171, 171, 8, 8, 1, 1, 3, 1, 3, 3, 3, 1, 1, 6, 8, 8, 23, 81, 81, 82, 82, 8, 8, 4, 4, 4, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 46, 24, 25, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 467 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581446 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581446 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581446/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581446 Building REAL300025581447 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581447' /scratch/stefan/7787361/working/building/REAL300025581447 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581447 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581447/0 /scratch/stefan/7787361/working/building/REAL300025581447 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/969 `/scratch/stefan/7787361/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=CC=C1NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581447 none CC(C)(C)C1=CC=CC=C1NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 199, 201, 201, 199, 65, 65, 92, 92, 34, 34, 34, 19, 8, 1, 1, 1, 1, 1, 1, 1, 92, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 92, 92, 34, 19, 19, 8, 8, 92, 92] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 683 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581447 none CC(C)(C)C1=CC=CC=C1NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 8, 7, 8, 8, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 25, 32, 92, 92, 92, 92, 92, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 1, 5, 25, 25, 32, 32, 1, 1] 201 rigid atoms, others: [43, 42, 11, 12, 13, 14, 15, 49, 50, 26, 27, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581447 none CC(C)(C)C1=CC=CC=C1NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 5, 5, 27, 27, 27, 96, 107, 201, 201, 201, 201, 201, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 8, 8, 27, 96, 96, 107, 107, 8, 8] 201 rigid atoms, others: [1, 4, 37, 6, 7, 8, 9, 10, 39, 40, 38, 5] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 576 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581447 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581447 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581447/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581447 Building REAL300025581448 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581448' /scratch/stefan/7787361/working/building/REAL300025581448 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581448 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581448/0 /scratch/stefan/7787361/working/building/REAL300025581448 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/970 `/scratch/stefan/7787361/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C2=NOC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)=C1) `REAL300025581448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581448 none COC1=CC=CC(C2=NOC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 195, 195, 195, 195, 96, 96, 96, 96, 57, 57, 57, 19, 8, 1, 1, 1, 1, 1, 1, 1, 96, 195, 201, 201, 201, 195, 195, 195, 57, 19, 19, 8, 8, 96, 195] 201 rigid atoms, others: [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]) total number of confs: 421 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581448 none COC1=CC=CC(C2=NOC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 11, 10, 11, 11, 1, 1, 1, 1, 1, 1, 6, 6, 6, 29, 34, 96, 96, 96, 96, 96, 1, 11, 19, 19, 19, 10, 11, 11, 6, 28, 28, 34, 34, 1, 11] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581448 none COC1=CC=CC(C2=NOC(C(=O)NCCC3=NC(=O)O[N-]3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 33, 33, 33, 100, 105, 195, 195, 195, 195, 195, 11, 1, 3, 3, 3, 1, 1, 1, 33, 100, 100, 105, 105, 11, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 23, 36, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 507 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581448 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581448 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581448/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581448 Building REAL300025581449 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581449' /scratch/stefan/7787361/working/building/REAL300025581449 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581449 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581449/0 /scratch/stefan/7787361/working/building/REAL300025581449 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/971 `/scratch/stefan/7787361/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2CCOCC2)C=C1) `REAL300025581449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581449 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 13, 37, 37, 111, 135, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 37, 111, 111, 135, 135, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 36, 37]) total number of confs: 639 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581449 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 23, 31, 101, 101, 101, 101, 101, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 6, 23, 23, 31, 31, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [1, 36, 37, 11, 12, 13, 14, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581449 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 24, 8, 1, 1, 1, 1, 1, 1, 1, 70, 101, 101, 101, 201, 201, 201, 201, 201, 101, 101, 70, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581449 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581449 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581449/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581449 Building REAL300025581450 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581450' /scratch/stefan/7787361/working/building/REAL300025581450 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581450 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581450/0 /scratch/stefan/7787361/working/building/REAL300025581450 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/972 `/scratch/stefan/7787361/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@@]2(C)CC[C@]1(C(=O)NCCC1=NC(=O)O[N-]1)OC2=O) `REAL300025581450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581450 none CC1(C)[C@@]2(C)CC[C@]1(C(=O)NCCC1=NC(=O)O[N-]1)OC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 170, 170, 170, 170, 170, 102, 102, 102, 25, 9, 1, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 170, 170, 170, 170, 170, 170, 170, 170, 170, 170, 170, 170, 102, 25, 25, 9, 9] 170 rigid atoms, others: [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, 39]) total number of confs: 414 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581450 none CC1(C)[C@@]2(C)CC[C@]1(C(=O)NCCC1=NC(=O)O[N-]1)OC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 58, 87, 170, 170, 170, 170, 170, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 11, 58, 58, 87, 87] 170 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 19, 20, 32, 33, 21, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 510 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581450 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581450 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581450/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581450 Building REAL300025581451 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581451' /scratch/stefan/7787361/working/building/REAL300025581451 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581451 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581451/0 /scratch/stefan/7787361/working/building/REAL300025581451 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/973 `/scratch/stefan/7787361/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1C2CC3=C(Br)C=CC=C3C21) `REAL300025581451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581451 none O=C(NCCC1=NC(=O)O[N-]1)C1C2CC3=C(Br)C=CC=C3C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 17, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 74, 106, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 74, 74, 106, 106, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 591 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581451 none O=C(NCCC1=NC(=O)O[N-]1)C1C2CC3=C(Br)C=CC=C3C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 17, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 24, 8, 1, 1, 1, 1, 1, 1, 1, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 24, 24, 8, 8, 200, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 616 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581451 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581451 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581451/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581451 Building REAL300025581452 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581452' /scratch/stefan/7787361/working/building/REAL300025581452 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581452 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581452/0 /scratch/stefan/7787361/working/building/REAL300025581452 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/974 `/scratch/stefan/7787361/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(C2=CC=CC=C2)O1) `REAL300025581452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581452 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 38, 38, 38, 107, 122, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 38, 107, 107, 122, 122, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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]) total number of confs: 599 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581452 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 72, 72, 72, 22, 8, 1, 1, 1, 1, 1, 1, 1, 187, 187, 187, 201, 201, 201, 201, 201, 187, 187, 187, 187, 72, 22, 22, 8, 8, 187, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 427 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581452 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 48, 64, 187, 187, 187, 187, 187, 1, 1, 1, 7, 7, 2, 7, 7, 1, 2, 2, 2, 10, 48, 48, 64, 64, 1, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581452 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581452 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581452/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581452 Building REAL300025581453 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581453' /scratch/stefan/7787361/working/building/REAL300025581453 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581453 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581453/0 /scratch/stefan/7787361/working/building/REAL300025581453 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/975 `/scratch/stefan/7787361/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CNC(=O)C2=CC=CC=C21) `REAL300025581453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581453 none O=C(NCCC1=NC(=O)O[N-]1)C1CNC(=O)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 67, 97, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 67, 67, 97, 97, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 570 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581453 none O=C(NCCC1=NC(=O)O[N-]1)C1CNC(=O)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 24, 8, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 25, 25, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 607 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581453 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581453 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581453/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581453 Building REAL300025581454 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581454' /scratch/stefan/7787361/working/building/REAL300025581454 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581454 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581454/0 /scratch/stefan/7787361/working/building/REAL300025581454 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/976 `/scratch/stefan/7787361/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(CC(=O)NCCC2=NC(=O)O[N-]2)N=C1C(F)(F)F) `REAL300025581454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581454 none CC1=CN(CC(=O)NCCC2=NC(=O)O[N-]2)N=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 116, 26, 26, 26, 12, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 116, 26, 12, 12, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 568 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581454 none CC1=CN(CC(=O)NCCC2=NC(=O)O[N-]2)N=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 32, 32, 32, 114, 114, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 6, 6, 32, 114, 114, 114, 114] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 588 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581454 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581454 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581454/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581454 Building REAL300025581455 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581455' /scratch/stefan/7787361/working/building/REAL300025581455 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581455 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581455/0 /scratch/stefan/7787361/working/building/REAL300025581455 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/977 `/scratch/stefan/7787361/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(N2CCCC2=O)=C1) `REAL300025581455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581455 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(N2CCCC2=O)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 19, 75, 89, 201, 201, 201, 201, 201, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 19, 75, 75, 89, 89, 8, 8, 1, 1, 1, 1, 1, 1, 8] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 518 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581455 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(N2CCCC2=O)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 40, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 5, 29, 29, 40, 40, 1, 1, 8, 8, 8, 8, 8, 8, 1] 201 rigid atoms, others: [1, 36, 11, 12, 13, 14, 15, 16, 22, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581455 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(N2CCCC2=O)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 19, 8, 1, 1, 1, 1, 1, 1, 1, 67, 137, 137, 137, 137, 132, 201, 201, 201, 201, 201, 137, 66, 19, 19, 8, 8, 137, 137, 201, 201, 201, 201, 201, 201, 137] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581455 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581455 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581455/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581455 Building REAL300025581456 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581456' /scratch/stefan/7787361/working/building/REAL300025581456 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581456 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581456/0 /scratch/stefan/7787361/working/building/REAL300025581456 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/978 `/scratch/stefan/7787361/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)OCC2=CC=CC=C2)C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581456 none CC1(C)CN(C(=O)OCC2=CC=CC=C2)C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 61, 61, 78, 78, 84, 201, 201, 201, 201, 201, 201, 45, 45, 45, 15, 8, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 61, 61, 201, 201, 201, 201, 201, 201, 201, 61, 45, 15, 15, 8, 8] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 772 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581456 none CC1(C)CN(C(=O)OCC2=CC=CC=C2)C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 21, 18, 21, 3, 1, 1, 1, 1, 1, 1, 1, 27, 27, 40, 40, 40, 114, 118, 201, 201, 201, 201, 201, 28, 28, 28, 28, 28, 28, 27, 27, 3, 3, 1, 1, 1, 1, 1, 27, 40, 114, 114, 118, 118] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41] 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, 34, 35, 36, 42, 43, 44, 45, 46, 47]) total number of confs: 601 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581456 none CC1(C)CN(C(=O)OCC2=CC=CC=C2)C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 27, 27, 23, 27, 27, 1, 1, 4, 4, 4, 15, 17, 61, 61, 61, 61, 61, 2, 2, 2, 2, 2, 2, 1, 1, 14, 14, 27, 27, 27, 27, 27, 1, 4, 15, 15, 17, 17] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 42, 34, 15, 16] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 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]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581456 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581456 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581456/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581456 Building REAL300025581457 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581457' /scratch/stefan/7787361/working/building/REAL300025581457 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581457 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581457/0 /scratch/stefan/7787361/working/building/REAL300025581457 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/979 `/scratch/stefan/7787361/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(COC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=N2)=N1) `REAL300025581457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581457 none CC1=NOC(COC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 121, 75, 57, 57, 57, 57, 31, 31, 31, 17, 8, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 121, 121, 57, 57, 31, 17, 17, 8, 8, 57] 201 rigid atoms, others: [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: 524 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581457 none CC1=NOC(COC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 9, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 19, 57, 57, 57, 57, 57, 1, 1, 36, 37, 37, 37, 9, 9, 1, 1, 5, 17, 17, 19, 19, 1] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581457 none CC1=NOC(COC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 30, 37, 37, 36, 36, 69, 69, 69, 124, 126, 201, 201, 201, 201, 201, 36, 36, 1, 2, 2, 2, 8, 8, 37, 37, 69, 124, 124, 126, 126, 36] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 636 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581457 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581457 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581457/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581457 Building REAL300025581458 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581458' /scratch/stefan/7787361/working/building/REAL300025581458 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581458 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581458/0 /scratch/stefan/7787361/working/building/REAL300025581458 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/980 `/scratch/stefan/7787361/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1CCCOC1) `REAL300025581458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581458 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 18, 77, 98, 201, 201, 201, 201, 201, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 18, 77, 77, 98, 98, 3, 3, 3, 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, 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]) total number of confs: 544 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581458 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 184, 84, 84, 84, 24, 8, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 201, 201, 201, 201, 201, 184, 184, 184, 184, 84, 24, 24, 8, 8, 184, 184, 184, 201, 201, 201, 201, 201, 201, 201, 201, 201] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 473 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581458 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C1CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 62, 85, 184, 184, 184, 184, 184, 1, 1, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 13, 62, 62, 85, 85, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 509 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581458 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581458 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581458/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581458 Building REAL300025581459 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581459' /scratch/stefan/7787361/working/building/REAL300025581459 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581459 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581459/0 /scratch/stefan/7787361/working/building/REAL300025581459 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/981 `/scratch/stefan/7787361/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2C=C(C(=O)NCCC3=NC(=O)O[N-]3)NC2=C(F)C=C1) `REAL300025581459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581459 none CC1=C2C=C(C(=O)NCCC3=NC(=O)O[N-]3)NC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 134, 73, 73, 73, 23, 8, 1, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134, 134, 134, 134, 134, 134, 134, 73, 23, 23, 8, 8, 134, 134, 134] 134 rigid atoms, others: [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]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581459 none CC1=C2C=C(C(=O)NCCC3=NC(=O)O[N-]3)NC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 13, 13, 12, 57, 72, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13, 57, 57, 72, 72, 1, 1, 1] 134 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 16, 17, 18, 19, 20, 21, 25, 33, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581459 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581459 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581459/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581459 Building REAL300025581460 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581460' /scratch/stefan/7787361/working/building/REAL300025581460 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581460 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581460/0 /scratch/stefan/7787361/working/building/REAL300025581460 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/982 `/scratch/stefan/7787361/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1)OCC1=CC=CC=C1) `REAL300025581460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581460 none O=C(NCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 18, 43, 50, 65, 65, 65, 132, 134, 201, 201, 201, 201, 201, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 18, 43, 43, 65, 132, 132, 134, 134, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [46, 47, 48, 49, 50, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 730 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581460 none O=C(NCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 102, 62, 34, 21, 21, 21, 9, 5, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 141, 141, 201, 201, 201, 201, 201, 201, 102, 62, 62, 21, 9, 9, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 823 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581460 none O=C(NCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 11, 4, 1, 1, 1, 3, 3, 3, 12, 13, 34, 34, 34, 34, 34, 1, 1, 1, 1, 18, 18, 32, 50, 50, 35, 50, 50, 11, 4, 4, 3, 12, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 50, 50, 50, 50, 50] 201 rigid atoms, others: [3, 4, 5, 38, 39, 40, 41, 42, 43, 16, 17, 18, 19, 36, 37] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581460 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581460 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581460/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581460 Building REAL300025581461 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581461' /scratch/stefan/7787361/working/building/REAL300025581461 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581461 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581461/0 /scratch/stefan/7787361/working/building/REAL300025581461 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/983 `/scratch/stefan/7787361/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1CC1CCCOC1) `REAL300025581461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581461 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1CC1CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 34, 34, 34, 104, 112, 201, 201, 201, 201, 201, 8, 8, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 34, 104, 104, 112, 112, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 567 number of broken/clashed sets: 51 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581461 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1CC1CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 62, 62, 63, 22, 8, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 195, 201, 201, 201, 201, 201, 142, 142, 142, 141, 62, 22, 22, 8, 8, 142, 142, 142, 196, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 686 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581461 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1CC1CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 11, 51, 59, 142, 142, 142, 142, 142, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 2, 2, 2, 1, 11, 50, 50, 59, 59, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 365 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581461 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581461 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581461/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581461 Building REAL300025581462 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581462' /scratch/stefan/7787361/working/building/REAL300025581462 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581462 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581462/0 /scratch/stefan/7787361/working/building/REAL300025581462 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/984 `/scratch/stefan/7787361/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1Br) `REAL300025581462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581462 none CC1=CC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 115, 115, 71, 71, 71, 24, 8, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 71, 24, 24, 8, 8, 115, 115, 115] 115 rigid atoms, others: [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]) total number of confs: 319 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581462 none CC1=CC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 51, 115, 115, 115, 115, 115, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 7, 37, 37, 51, 51, 2, 2, 2] 115 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581462 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581462 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581462/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581462 Building REAL300025581463 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581463' /scratch/stefan/7787361/working/building/REAL300025581463 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581463 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581463/0 /scratch/stefan/7787361/working/building/REAL300025581463 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/985 `/scratch/stefan/7787361/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1COCC1=CC=CC=C1) `REAL300025581463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581463 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1COCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 55, 55, 117, 117, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 30, 13, 3, 1, 1, 1, 1, 1, 1, 1, 55, 117, 117, 117, 117, 32, 32, 33, 32, 30, 30, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 659 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581463 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1COCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 23, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 1, 3, 9, 21, 33, 33, 31, 33, 33, 7, 21, 21, 23, 23, 1, 1, 1, 1, 3, 3, 20, 20, 33, 33, 32, 33, 33] 201 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581463 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1COCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 5, 1, 1, 1, 1, 1, 1, 1, 17, 56, 56, 35, 56, 56, 56, 74, 102, 201, 201, 201, 201, 201, 201, 17, 7, 7, 5, 5, 56, 56, 35, 56, 74, 74, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581463 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581463 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581463/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581463 Building REAL300025581464 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581464' /scratch/stefan/7787361/working/building/REAL300025581464 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581464 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581464/0 /scratch/stefan/7787361/working/building/REAL300025581464 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/986 `/scratch/stefan/7787361/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1OC(F)(F)F) `REAL300025581464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581464 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 12, 53, 54, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 12, 53, 53, 54, 54, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 379 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581464 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 51, 155, 155, 155, 147, 155, 155, 155, 201, 201, 201, 201, 51, 17, 17, 8, 8, 155, 155, 155] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581464 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581464 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581464/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581464 Building REAL300025581465 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581465' /scratch/stefan/7787361/working/building/REAL300025581465 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581465 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581465/0 /scratch/stefan/7787361/working/building/REAL300025581465 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/987 `/scratch/stefan/7787361/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2CC2)NC(C2CC2)=C1) `REAL300025581465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581465 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2CC2)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 19, 19, 57, 57, 133, 133, 133, 133, 133, 7, 1, 1, 1, 1, 7, 6, 7, 33, 33, 6, 19, 57, 57, 57, 57, 1, 1, 1, 1, 1, 7, 33, 33, 33, 33, 33, 7] 201 rigid atoms, others: [12, 13, 14, 15, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 384 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581465 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2CC2)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 28, 31, 93, 93, 93, 93, 93, 1, 1, 1, 7, 7, 1, 1, 1, 10, 10, 1, 6, 27, 27, 31, 31, 7, 7, 7, 7, 7, 1, 10, 10, 10, 10, 10, 1] 201 rigid atoms, others: [32, 1, 38, 11, 12, 13, 16, 17, 18, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581465 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2CC2)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 1, 1, 1, 1, 1, 1, 1, 37, 93, 93, 134, 134, 93, 93, 93, 164, 164, 93, 37, 16, 16, 8, 8, 134, 134, 134, 134, 134, 93, 164, 164, 164, 164, 164, 93] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581465 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2CC2)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 10, 32, 32, 81, 85, 165, 165, 165, 165, 165, 10, 10, 10, 35, 35, 10, 1, 1, 1, 1, 10, 32, 81, 81, 85, 85, 35, 35, 35, 35, 35, 10, 1, 1, 1, 1, 1, 10] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38]) total number of confs: 499 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581465 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581465 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581465/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581465 Building REAL300025581466 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581466' /scratch/stefan/7787361/working/building/REAL300025581466 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581466 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581466/0 /scratch/stefan/7787361/working/building/REAL300025581466 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/988 `/scratch/stefan/7787361/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CCO[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581466 none CC(C)(C)OC(=O)N[C@@H]1CCO[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 166, 135, 166, 99, 99, 99, 99, 99, 99, 52, 99, 52, 52, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 99, 99, 99, 99, 52, 19, 19, 8, 8] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 643 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581466 none CC(C)(C)OC(=O)N[C@@H]1CCO[C@@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 16, 16, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 36, 99, 99, 99, 99, 99, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 6, 28, 28, 36, 36] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581466 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581466 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581466/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581466 Building REAL300025581467 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581467' /scratch/stefan/7787361/working/building/REAL300025581467 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581467 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581467/0 /scratch/stefan/7787361/working/building/REAL300025581467 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/989 `/scratch/stefan/7787361/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2C1) `REAL300025581467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581467 none CC(C)(C)OC(=O)NC1CC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 197, 157, 197, 72, 72, 72, 72, 72, 72, 30, 30, 30, 15, 7, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 72, 72, 72, 72, 72, 30, 15, 15, 7, 7, 72, 72, 72] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 599 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581467 none CC(C)(C)OC(=O)NC1CC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 11, 6, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 26, 72, 72, 72, 72, 72, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 5, 23, 23, 26, 26, 1, 1, 1] 201 rigid atoms, others: [11, 49, 38, 7, 8, 9, 10, 39, 12, 13, 14, 48, 40, 50, 41, 25, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581467 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581467 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581467/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581467 Building REAL300025581468 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581468' /scratch/stefan/7787361/working/building/REAL300025581468 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581468 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581468/0 /scratch/stefan/7787361/working/building/REAL300025581468 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/990 `/scratch/stefan/7787361/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL300025581468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581468 none CC(C)(C)OC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 201, 201, 118, 118, 119, 119, 119, 76, 76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 75, 24, 24, 8, 8] 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]) total number of confs: 495 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581468 none CC(C)(C)OC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 21, 31, 118, 118, 118, 119, 119, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 4, 20, 20, 31, 31] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 21, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581468 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581468 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581468/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581468 Building REAL300025581469 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581469' /scratch/stefan/7787361/working/building/REAL300025581469 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581469 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581469/0 /scratch/stefan/7787361/working/building/REAL300025581469 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/991 `/scratch/stefan/7787361/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(O)CN(C(=O)OCC2=CC=CC=C2)C1) `REAL300025581469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581469 none O=C(NCCC1=NC(=O)O[N-]1)C1(O)CN(C(=O)OCC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [75, 31, 75, 75, 141, 141, 201, 201, 201, 201, 201, 31, 31, 31, 17, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 31, 75, 141, 141, 141, 141, 96, 31, 31, 3, 3, 1, 1, 1, 1, 1, 31, 31] 603 rigid atoms, others: [36, 37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 712 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581469 none O=C(NCCC1=NC(=O)O[N-]1)C1(O)CN(C(=O)OCC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 26, 27, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 2, 2, 2, 14, 31, 31, 17, 31, 31, 1, 7, 26, 26, 27, 27, 6, 1, 1, 14, 14, 31, 31, 31, 31, 31, 1, 1] 603 rigid atoms, others: [32, 1, 33, 41, 42, 11, 12, 13, 14, 15, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581469 none O=C(NCCC1=NC(=O)O[N-]1)C1(O)CN(C(=O)OCC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 11, 6, 1, 1, 1, 1, 1, 1, 1, 27, 66, 66, 66, 66, 105, 105, 105, 201, 201, 201, 201, 201, 201, 66, 27, 11, 11, 6, 6, 198, 66, 66, 201, 201, 201, 201, 201, 201, 201, 66, 66] 603 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 979 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581469 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581469 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581469/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581469 Building REAL300025581470 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581470' /scratch/stefan/7787361/working/building/REAL300025581470 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581470 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581470/0 /scratch/stefan/7787361/working/building/REAL300025581470 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/992 `/scratch/stefan/7787361/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CCSCC1) `REAL300025581470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581470 none CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 197, 55, 197, 39, 39, 39, 15, 8, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 39, 15, 15, 8, 8, 55, 55, 55, 55, 55, 55, 55, 55] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 564 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581470 none CC(C)(C)OC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 7, 1, 7, 1, 1, 3, 3, 3, 13, 17, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 13, 13, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 5, 38, 7, 8, 41, 42, 39, 44, 45, 40, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581470 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581470 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581470/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581470 Building REAL300025581471 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581471' /scratch/stefan/7787361/working/building/REAL300025581471 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581471 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581471/0 /scratch/stefan/7787361/working/building/REAL300025581471 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/993 `/scratch/stefan/7787361/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(C#N)C=C1) `REAL300025581471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581471 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(C#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 23, 23, 23, 88, 94, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 23, 88, 88, 94, 94, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 33, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 524 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581471 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(C#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 169, 53, 53, 19, 8, 1, 1, 1, 1, 1, 1, 1, 169, 201, 201, 201, 201, 201, 201, 201, 169, 169, 169, 169, 169, 169, 53, 19, 19, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581471 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581471 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581471/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581471 Building REAL300025581472 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581472' /scratch/stefan/7787361/working/building/REAL300025581472 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581472 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581472/0 /scratch/stefan/7787361/working/building/REAL300025581472 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/994 `/scratch/stefan/7787361/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(COCC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025581472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581472 none N#CC1=CC=C(COCC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 201, 201, 177, 115, 99, 48, 48, 48, 16, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 177, 177, 99, 99, 48, 16, 16, 8, 8, 201, 201] 201 rigid atoms, others: [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: 844 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581472 none N#CC1=CC=C(COCC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 24, 48, 51, 51, 51, 121, 123, 201, 201, 201, 201, 201, 1, 1, 1, 1, 8, 8, 48, 48, 51, 121, 121, 123, 123, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 34, 20, 21, 22, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 637 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581472 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581472 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581472/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581472 Building REAL300025581473 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581473' /scratch/stefan/7787361/working/building/REAL300025581473 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581473 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581473/0 /scratch/stefan/7787361/working/building/REAL300025581473 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/995 `/scratch/stefan/7787361/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(COCC(=O)NCCC2=NC(=O)O[N-]2)=CC=N1) `REAL300025581473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581473 none COC1=CC(COCC(=O)NCCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 155, 111, 99, 47, 47, 47, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 155, 155, 99, 99, 47, 15, 15, 7, 7, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 726 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581473 none COC1=CC(COCC(=O)NCCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 24, 42, 48, 48, 48, 120, 120, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 8, 8, 42, 42, 48, 120, 120, 120, 120, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 25, 36] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581473 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581473 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581473/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581473 Building REAL300025581474 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581474' /scratch/stefan/7787361/working/building/REAL300025581474 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581474 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581474/0 /scratch/stefan/7787361/working/building/REAL300025581474 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/996 `/scratch/stefan/7787361/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(COCC(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025581474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581474 none COC1=CC=C(COCC(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 136, 89, 79, 43, 43, 43, 13, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 136, 136, 79, 79, 43, 13, 13, 7, 7, 201] 201 rigid atoms, others: [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: 669 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581474 none COC1=CC=C(COCC(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 22, 40, 46, 46, 46, 113, 117, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 6, 6, 40, 40, 46, 113, 113, 117, 117, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 25, 26, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 654 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581474 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581474 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581474/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581474 Building REAL300025581475 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581475' /scratch/stefan/7787361/working/building/REAL300025581475 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581475 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581475/0 /scratch/stefan/7787361/working/building/REAL300025581475 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/997 `/scratch/stefan/7787361/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C2CCOC2)=N1) `REAL300025581475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581475 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C2CCOC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 5, 5, 5, 12, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 41, 41, 41, 126, 132, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 41, 126, 126, 132, 132, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 30, 31] 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]) total number of confs: 609 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581475 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C2CCOC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 5, 5, 5, 12, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 54, 54, 54, 19, 8, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 201, 201, 201, 201, 129, 129, 129, 129, 54, 19, 19, 8, 8, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 524 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581475 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C2CCOC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 5, 5, 5, 12, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 40, 47, 129, 129, 129, 129, 129, 1, 1, 1, 9, 9, 9, 9, 1, 2, 2, 2, 8, 40, 40, 47, 47, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581475 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581475 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581475/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581475 Building REAL300025581476 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581476' /scratch/stefan/7787361/working/building/REAL300025581476 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581476 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581476/0 /scratch/stefan/7787361/working/building/REAL300025581476 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/998 `/scratch/stefan/7787361/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=C(Br)C=NC=C2C=C1) `REAL300025581476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581476 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=C(Br)C=NC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 17, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 61, 86, 164, 164, 164, 164, 164, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 61, 61, 86, 86, 1, 1, 1, 1] 164 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 474 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581476 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=C(Br)C=NC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 17, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 3, 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: [96, 96, 24, 8, 1, 1, 1, 1, 1, 1, 1, 96, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 96, 25, 25, 8, 8, 164, 164, 164, 164] 164 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581476 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581476 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581476/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581476 Building REAL300025581477 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581477' /scratch/stefan/7787361/working/building/REAL300025581477 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581477 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581477/0 /scratch/stefan/7787361/working/building/REAL300025581477 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/999 `/scratch/stefan/7787361/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C(O)C1=CC(Cl)=CC(Cl)=C1) `REAL300025581477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581477 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C(O)C1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 270 conformations in input total number of sets (complete confs): 270 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 13, 13, 13, 38, 38, 90, 90, 90, 90, 90, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 38, 38, 38, 38, 2, 6, 1, 1, 1] 270 rigid atoms, others: [37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 234 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581477 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C(O)C1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [175, 75, 175, 75, 76, 20, 8, 1, 1, 1, 1, 1, 1, 1, 176, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 176, 175, 175, 75, 20, 20, 8, 8, 201, 603, 201, 201, 201] 603 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1433 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581477 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581477 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581477/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581477 Building REAL300025581478 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581478' /scratch/stefan/7787361/working/building/REAL300025581478 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581478 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581478/0 /scratch/stefan/7787361/working/building/REAL300025581478 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1000 `/scratch/stefan/7787361/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC(Cl)=CC(Cl)=C1)NCCC1=NC(=O)O[N-]1) `REAL300025581478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581478 none O=C(CC1=CC(Cl)=CC(Cl)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 16, 1, 1, 16, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 157, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 63, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 702 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581478 none O=C(CC1=CC(Cl)=CC(Cl)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 16, 1, 1, 16, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 80, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 11, 63, 63, 80, 80] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 498 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581478 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581478 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581478/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581478 Building REAL300025581479 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581479' /scratch/stefan/7787361/working/building/REAL300025581479 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581479 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581479/0 /scratch/stefan/7787361/working/building/REAL300025581479 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1001 `/scratch/stefan/7787361/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C([N+](=O)[O-])C=C2F)C=C1) `REAL300025581479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581479 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 26, 26, 94, 115, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 26, 94, 94, 115, 115, 1, 1, 1, 9, 9] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 586 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581479 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 39, 59, 145, 145, 145, 145, 145, 1, 1, 1, 1, 9, 9, 2, 8, 9, 9, 9, 9, 9, 1, 1, 9, 39, 39, 59, 59, 9, 9, 9, 1, 1] 201 rigid atoms, others: [1, 34, 35, 11, 12, 13, 14, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 405 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581479 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 23, 8, 1, 1, 1, 1, 1, 1, 1, 88, 145, 145, 145, 201, 201, 197, 201, 201, 201, 201, 201, 201, 145, 145, 88, 23, 23, 8, 8, 201, 201, 201, 145, 145] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581479 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581479 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581479/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581479 Building REAL300025581480 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581480' /scratch/stefan/7787361/working/building/REAL300025581480 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581480 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581480/0 /scratch/stefan/7787361/working/building/REAL300025581480 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1002 `/scratch/stefan/7787361/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(C=CC(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025581480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581480 none CSC1=CC=C(C=CC(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 129, 129, 129, 129, 57, 57, 40, 40, 40, 17, 8, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 201, 129, 129, 57, 57, 40, 17, 17, 8, 8] 201 rigid atoms, others: [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: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581480 none CSC1=CC=C(C=CC(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 9, 9, 20, 20, 20, 50, 52, 129, 129, 129, 129, 129, 1, 11, 11, 11, 1, 1, 9, 9, 20, 50, 50, 52, 52] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 23, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581480 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581480 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581480/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581480 Building REAL300025581481 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581481' /scratch/stefan/7787361/working/building/REAL300025581481 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581481 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581481/0 /scratch/stefan/7787361/working/building/REAL300025581481 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1003 `/scratch/stefan/7787361/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=CC=CC=C2Br)S1) `REAL300025581481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581481 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=CC=CC=C2Br)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 9, 35, 35, 118, 133, 201, 201, 201, 201, 201, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 35, 118, 118, 133, 133, 9, 1, 1, 1, 1] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 611 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581481 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=CC=CC=C2Br)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 44, 56, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 9, 9, 1, 9, 9, 9, 1, 9, 44, 44, 56, 56, 1, 9, 9, 1, 9] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 22, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581481 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2=CC=CC=C2Br)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 23, 8, 1, 1, 1, 1, 1, 1, 1, 70, 147, 147, 147, 147, 201, 201, 192, 201, 201, 201, 147, 70, 23, 23, 8, 8, 147, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581481 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581481 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581481/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581481 Building REAL300025581482 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581482' /scratch/stefan/7787361/working/building/REAL300025581482 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581482 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581482/0 /scratch/stefan/7787361/working/building/REAL300025581482 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1004 `/scratch/stefan/7787361/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCN1CC1=CC=C(Cl)C=C1) `REAL300025581482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581482 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCN1CC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 5, 15, 15, 69, 96, 191, 191, 191, 191, 191, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 15, 69, 69, 96, 96, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1] 191 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]) total number of confs: 553 number of broken/clashed sets: 60 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581482 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCN1CC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 27, 45, 165, 165, 165, 165, 165, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 27, 27, 45, 45, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5] 191 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41]) total number of confs: 350 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581482 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCN1CC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 99, 165, 165, 165, 165, 165, 191, 191, 191, 191, 191, 191, 191, 98, 24, 24, 8, 8, 165, 165, 165, 165, 165, 165, 165, 191, 191, 191, 191, 191, 191] 191 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 676 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581482 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581482 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581482/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581482 Building REAL300025581483 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581483' /scratch/stefan/7787361/working/building/REAL300025581483 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581483 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581483/0 /scratch/stefan/7787361/working/building/REAL300025581483 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1005 `/scratch/stefan/7787361/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025581483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581483 none CC(C)(C)OC(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 165, 157, 165, 101, 101, 101, 101, 51, 51, 51, 17, 8, 1, 1, 1, 1, 1, 1, 1, 101, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 101, 101, 51, 17, 17, 8, 8, 101] 201 rigid atoms, others: [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]) total number of confs: 531 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581483 none CC(C)(C)OC(=O)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 17, 19, 19, 9, 6, 9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 27, 31, 101, 101, 101, 101, 101, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 5, 27, 27, 31, 31, 1] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581483 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581483 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581483/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581483 Building REAL300025581484 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581484' /scratch/stefan/7787361/working/building/REAL300025581484 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581484 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581484/0 /scratch/stefan/7787361/working/building/REAL300025581484 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1006 `/scratch/stefan/7787361/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)C2=CC=CC=C2O1) `REAL300025581484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581484 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 41, 73, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 73, 73, 1, 1, 1, 1] 151 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 441 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581484 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Br)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [71, 71, 24, 8, 1, 1, 1, 1, 1, 1, 1, 71, 151, 151, 151, 151, 151, 151, 151, 151, 151, 71, 24, 24, 8, 8, 151, 151, 151, 151] 151 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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/7787361/working/building/REAL300025581484 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581484 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581484/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581484 Building REAL300025581485 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581485' /scratch/stefan/7787361/working/building/REAL300025581485 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581485 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581485/0 /scratch/stefan/7787361/working/building/REAL300025581485 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1007 `/scratch/stefan/7787361/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(N2CCCC2)=N1) `REAL300025581485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581485 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(N2CCCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 20, 37, 39, 65, 65, 65, 65, 65, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 20, 37, 37, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1] 65 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 189 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581485 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(N2CCCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 20, 24, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 20, 20, 24, 24, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8] 65 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 21, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581485 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(N2CCCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 13, 8, 1, 1, 1, 1, 1, 1, 1, 46, 58, 58, 58, 58, 58, 65, 65, 65, 65, 58, 46, 14, 13, 8, 8, 58, 58, 65, 65, 65, 65, 65, 65, 65, 65] 65 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581485 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581485 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581485/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581485 Building REAL300025581486 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581486' /scratch/stefan/7787361/working/building/REAL300025581486 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581486 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581486/0 /scratch/stefan/7787361/working/building/REAL300025581486 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1008 `/scratch/stefan/7787361/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(I)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL300025581486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581486 none CN1C=C(I)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'I', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 18, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 160, 160, 98, 98, 98, 24, 8, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 160, 98, 24, 24, 8, 8] 160 rigid atoms, others: [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]) total number of confs: 390 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581486 none CN1C=C(I)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'I', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 18, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 64, 160, 160, 160, 160, 160, 1, 2, 2, 2, 1, 7, 37, 37, 64, 64] 160 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 21] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581486 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581486 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581486/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581486 Building REAL300025581487 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581487' /scratch/stefan/7787361/working/building/REAL300025581487 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581487 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581487/0 /scratch/stefan/7787361/working/building/REAL300025581487 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1009 `/scratch/stefan/7787361/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=NN2C(C(F)(F)F)=C1) `REAL300025581487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581487 none CC1=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=NN2C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 167, 88, 88, 88, 24, 8, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 88, 24, 24, 8, 8, 167] 167 rigid atoms, others: [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]) total number of confs: 392 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581487 none CC1=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=NN2C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 61, 88, 167, 167, 167, 167, 167, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 12, 61, 61, 88, 88, 1] 167 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 17, 18, 19, 20, 24, 25, 26, 27, 28] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 29, 30, 31]) total number of confs: 507 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581487 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581487 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581487/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581487 Building REAL300025581488 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581488' /scratch/stefan/7787361/working/building/REAL300025581488 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581488 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581488/0 /scratch/stefan/7787361/working/building/REAL300025581488 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1010 `/scratch/stefan/7787361/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1=CC=C(Br)C=N1)NCCC1=NC(=O)O[N-]1) `REAL300025581488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581488 none O=C(COC1=CC=C(Br)C=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 17, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 36, 130, 193, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 130, 130, 201, 201, 201, 35, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 566 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581488 none O=C(COC1=CC=C(Br)C=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 17, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 3, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 137, 137, 201, 201, 201, 201, 201, 18, 18, 1, 1, 1, 80, 137, 137, 137, 137] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581488 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581488 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581488/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581488 Building REAL300025581489 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581489' /scratch/stefan/7787361/working/building/REAL300025581489 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581489 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581489/0 /scratch/stefan/7787361/working/building/REAL300025581489 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1011 `/scratch/stefan/7787361/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCN2C=C(C(F)(F)F)N=C12) `REAL300025581489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581489 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCN2C=C(C(F)(F)F)N=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 8, 1, 1, 5, 15, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 1, 13, 13, 66, 93, 186, 186, 186, 186, 186, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 13, 66, 66, 93, 93, 1, 1, 1, 1, 1, 1, 1, 1] 186 rigid atoms, others: [32, 1, 34, 35, 36, 33, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 543 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581489 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCN2C=C(C(F)(F)F)N=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 8, 1, 1, 5, 15, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [86, 86, 24, 8, 1, 1, 1, 1, 1, 1, 1, 86, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 86, 25, 25, 8, 8, 186, 186, 186, 186, 186, 186, 186, 186] 186 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 583 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581489 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581489 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581489/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581489 Building REAL300025581490 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581490' /scratch/stefan/7787361/working/building/REAL300025581490 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581490 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581490/0 /scratch/stefan/7787361/working/building/REAL300025581490 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1012 `/scratch/stefan/7787361/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC(Cl)=CC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1) `REAL300025581490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581490 none O=C(CC1=CC(Cl)=CC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 15, 8, 1, 1, 1, 1, 1, 1, 1, 140, 140, 201, 201, 201, 201, 201, 201, 43, 15, 15, 8, 8] 201 rigid atoms, others: [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: 604 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581490 none O=C(CC1=CC(Cl)=CC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 101, 103, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 32, 101, 101, 103, 103] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30] set([0, 1, 34, 35, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 554 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581490 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581490 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581490/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581490 Building REAL300025581491 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581491' /scratch/stefan/7787361/working/building/REAL300025581491 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581491 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581491/0 /scratch/stefan/7787361/working/building/REAL300025581491 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1013 `/scratch/stefan/7787361/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1N1CCOCC1) `REAL300025581491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581491 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 3, 3, 3, 3, 4, 15, 15, 15, 82, 107, 192, 192, 192, 192, 192, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 3, 3, 15, 82, 82, 107, 107, 3, 1, 1, 1, 1, 1, 1, 1, 1] 192 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 566 number of broken/clashed sets: 67 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581491 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [167, 167, 167, 167, 71, 71, 72, 22, 8, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 192, 192, 192, 192, 192, 167, 167, 167, 167, 167, 71, 22, 22, 8, 8, 167, 192, 192, 192, 192, 192, 192, 192, 192] 192 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 426 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581491 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 35, 57, 167, 167, 167, 167, 167, 1, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 7, 35, 35, 57, 57, 1, 3, 3, 3, 3, 3, 4, 3, 3] 192 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 16, 17, 18, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 409 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581491 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581491 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581491/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581491 Building REAL300025581492 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581492' /scratch/stefan/7787361/working/building/REAL300025581492 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581492 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581492/0 /scratch/stefan/7787361/working/building/REAL300025581492 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1014 `/scratch/stefan/7787361/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC(Cl)=C1F) `REAL300025581492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581492 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC(Cl)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 16, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 13, 65, 91, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 65, 65, 91, 91, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 548 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581492 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC(Cl)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 16, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 97, 201, 201, 201, 149, 201, 201, 201, 201, 97, 25, 25, 8, 8, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 694 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581492 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581492 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581492/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581492 Building REAL300025581493 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581493' /scratch/stefan/7787361/working/building/REAL300025581493 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581493 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581493/0 /scratch/stefan/7787361/working/building/REAL300025581493 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1015 `/scratch/stefan/7787361/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(NC2=NC=CC(C(F)(F)F)=N2)=C1) `REAL300025581493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581493 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(NC2=NC=CC(C(F)(F)F)=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 31, 51, 51, 124, 124, 201, 201, 201, 201, 201, 31, 31, 31, 31, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 31, 51, 124, 124, 124, 124, 31, 31, 31, 10, 1, 1, 31] 201 rigid atoms, others: [37, 38, 16, 17, 18, 19, 20, 21, 22, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 610 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581493 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(NC2=NC=CC(C(F)(F)F)=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 13, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 12, 31, 31, 12, 31, 31, 31, 31, 31, 31, 1, 3, 13, 13, 13, 13, 1, 1, 1, 12, 31, 12, 1] 201 rigid atoms, others: [1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 39, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581493 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(NC2=NC=CC(C(F)(F)F)=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 15, 7, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 133, 201, 201, 133, 201, 201, 201, 201, 201, 201, 50, 36, 15, 15, 7, 7, 50, 50, 50, 133, 201, 133, 50] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581493 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581493 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581493/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581493 Building REAL300025581494 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581494' /scratch/stefan/7787361/working/building/REAL300025581494 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581494 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581494/0 /scratch/stefan/7787361/working/building/REAL300025581494 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1016 `/scratch/stefan/7787361/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C=C(C(=O)NCCC3=NC(=O)O[N-]3)SC2=C1) `REAL300025581494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581494 none COC1=CC=C2C=C(C(=O)NCCC3=NC(=O)O[N-]3)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 190, 190, 191, 191, 191, 191, 81, 82, 82, 24, 8, 1, 1, 1, 1, 1, 1, 1, 190, 190, 190, 201, 201, 201, 191, 191, 191, 81, 24, 24, 8, 8, 190] 201 rigid atoms, others: [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: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581494 none COC1=CC=C2C=C(C(=O)NCCC3=NC(=O)O[N-]3)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 63, 89, 190, 190, 190, 190, 190, 1, 1, 1, 3, 3, 3, 1, 1, 1, 11, 63, 63, 89, 89, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 33, 19, 20, 21, 25, 26, 27] set([0, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 518 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581494 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581494 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581494/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581494 Building REAL300025581495 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581495' /scratch/stefan/7787361/working/building/REAL300025581495 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581495 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581495/0 /scratch/stefan/7787361/working/building/REAL300025581495 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1017 `/scratch/stefan/7787361/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(CC(=O)NCCC3=NC(=O)O[N-]3)=COC2=C1C) `REAL300025581495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581495 none COC1=CC=C2C(CC(=O)NCCC3=NC(=O)O[N-]3)=COC2=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 116, 38, 38, 38, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 116, 38, 15, 15, 7, 7, 201, 201, 201, 201] 201 rigid atoms, others: [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, 39]) total number of confs: 589 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581495 none COC1=CC=C2C(CC(=O)NCCC3=NC(=O)O[N-]3)=COC2=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 30, 30, 30, 102, 104, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 7, 7, 30, 102, 102, 104, 104, 1, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 36, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581495 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581495 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581495/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581495 Building REAL300025581496 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581496' /scratch/stefan/7787361/working/building/REAL300025581496 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581496 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581496/0 /scratch/stefan/7787361/working/building/REAL300025581496 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1018 `/scratch/stefan/7787361/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(OC2=CC=CC=C2)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL300025581496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581496 none CC1=CC(OC2=CC=CC=C2)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 44, 44, 193, 201, 201, 193, 201, 201, 68, 68, 27, 27, 27, 13, 7, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 201, 201, 193, 201, 201, 68, 68, 27, 13, 13, 7, 7] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581496 none CC1=CC(OC2=CC=CC=C2)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 5, 5, 31, 31, 43, 121, 121, 201, 201, 201, 201, 201, 11, 11, 11, 11, 1, 1, 1, 1, 1, 11, 11, 40, 119, 118, 121, 121] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 645 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581496 none CC1=CC(OC2=CC=CC=C2)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 11, 11, 9, 11, 11, 1, 1, 1, 1, 9, 9, 9, 30, 30, 68, 68, 68, 68, 68, 2, 2, 2, 1, 11, 11, 9, 11, 11, 1, 1, 9, 30, 30, 30, 30] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14, 34, 35, 28] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581496 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581496 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581496/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581496 Building REAL300025581497 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581497' /scratch/stefan/7787361/working/building/REAL300025581497 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581497 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581497/0 /scratch/stefan/7787361/working/building/REAL300025581497 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1019 `/scratch/stefan/7787361/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCC2=NC(=O)O[N-]2)OC2=CC=CC=C2NC1=O) `REAL300025581497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581497 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)OC2=CC=CC=C2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 81, 81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 81, 24, 24, 8, 8, 167, 167, 167, 167, 167] 167 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 529 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581497 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)OC2=CC=CC=C2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 13, 13, 13, 62, 83, 167, 167, 167, 167, 167, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 62, 62, 83, 83, 1, 1, 1, 1, 1] 167 rigid atoms, others: [0, 1, 2, 34, 33, 35, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581497 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581497 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581497/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581497 Building REAL300025581498 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581498' /scratch/stefan/7787361/working/building/REAL300025581498 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581498 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581498/0 /scratch/stefan/7787361/working/building/REAL300025581498 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1020 `/scratch/stefan/7787361/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CSC(COC2=CC=CC=C2)=N1)NCCC1=NC(=O)O[N-]1) `REAL300025581498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581498 none O=C(CC1=CSC(COC2=CC=CC=C2)=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 105, 110, 110, 110, 110, 201, 201, 201, 201, 201, 201, 201, 110, 8, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 110, 201, 201, 201, 201, 201, 201, 201, 37, 9, 9, 8, 8] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 801 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581498 none O=C(CC1=CSC(COC2=CC=CC=C2)=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 21, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 56, 56, 112, 112, 201, 201, 201, 201, 201, 21, 21, 9, 2, 2, 1, 1, 1, 1, 1, 56, 112, 112, 112, 112] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 30, 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, 35, 36, 37, 38, 39]) total number of confs: 620 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581498 none O=C(CC1=CSC(COC2=CC=CC=C2)=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 11, 11, 36, 36, 110, 110, 110, 110, 110, 5, 5, 1, 9, 9, 9, 9, 9, 9, 9, 11, 36, 36, 36, 36] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581498 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581498 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581498/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581498 Building REAL300025581499 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581499' /scratch/stefan/7787361/working/building/REAL300025581499 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581499 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581499/0 /scratch/stefan/7787361/working/building/REAL300025581499 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1021 `/scratch/stefan/7787361/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NC2=C(Cl)C=CC=C12) `REAL300025581499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581499 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NC2=C(Cl)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 81, 81, 81, 20, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 80, 21, 21, 8, 8, 127, 127, 127, 127] 127 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581499 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NC2=C(Cl)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 44, 62, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 44, 44, 62, 62, 1, 1, 1, 1] 127 rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581499 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581499 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581499/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581499 Building REAL300025581500 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581500' /scratch/stefan/7787361/working/building/REAL300025581500 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581500 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581500/0 /scratch/stefan/7787361/working/building/REAL300025581500 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1022 `/scratch/stefan/7787361/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C1=CN(C)N=C1) `REAL300025581500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581500 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 7, 24, 24, 24, 100, 106, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 24, 100, 100, 106, 106, 7, 1, 2, 2, 2, 1] 201 rigid atoms, others: [35, 39, 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, 36, 37, 38]) total number of confs: 548 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581500 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 58, 58, 58, 19, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 201, 201, 201, 201, 201, 131, 131, 131, 131, 131, 58, 19, 19, 8, 8, 131, 201, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 442 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581500 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 35, 131, 131, 131, 131, 131, 1, 1, 1, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 5, 29, 29, 35, 35, 1, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 16, 17, 18, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 267 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581500 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581500 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581500/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581500 Building REAL300025581501 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581501' /scratch/stefan/7787361/working/building/REAL300025581501 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581501 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581501/0 /scratch/stefan/7787361/working/building/REAL300025581501 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1023 `/scratch/stefan/7787361/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=N1) `REAL300025581501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581501 none CC(C)(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 147, 201, 201, 147, 147, 66, 66, 66, 19, 8, 1, 1, 1, 1, 1, 1, 1, 147, 147, 147, 146, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 65, 19, 19, 8, 8, 147] 201 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, 37]) total number of confs: 665 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581501 none CC(C)(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 29, 47, 147, 147, 147, 147, 147, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 5, 29, 29, 47, 47, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 18, 19, 20, 21, 37, 31] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581501 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581501 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581501/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581501 Building REAL300025581502 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581502' /scratch/stefan/7787361/working/building/REAL300025581502 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581502 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581502/0 /scratch/stefan/7787361/working/building/REAL300025581502 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1024 `/scratch/stefan/7787361/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CN=C1F) `REAL300025581502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581502 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CN=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 8, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 66, 86, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 13, 66, 66, 86, 86, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 520 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581502 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Br)=CN=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 8, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 8, 1, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 201, 201, 201, 201, 85, 20, 20, 8, 8, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581502 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581502 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581502/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581502 Building REAL300025581503 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581503' /scratch/stefan/7787361/working/building/REAL300025581503 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581503 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581503/0 /scratch/stefan/7787361/working/building/REAL300025581503 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1025 `/scratch/stefan/7787361/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(C(F)C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025581503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581503 none CC(C)(C)OC(=O)N1CCC(C(F)C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 152, 110, 152, 110, 110, 110, 83, 37, 86, 37, 37, 8, 8, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 110, 110, 86, 36, 9, 9, 8, 8, 110, 110] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 667 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581503 none CC(C)(C)OC(=O)N1CCC(C(F)C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 58, 58, 110, 110, 110, 110, 110, 1, 8, 8, 8, 7, 7, 7, 8, 8, 8, 1, 1, 1, 1, 1, 6, 22, 58, 58, 58, 58, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 45, 46, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581503 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581503 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581503/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581503 Building REAL300025581504 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581504' /scratch/stefan/7787361/working/building/REAL300025581504 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581504 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581504/0 /scratch/stefan/7787361/working/building/REAL300025581504 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1026 `/scratch/stefan/7787361/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)CC(C)O1) `REAL300025581504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581504 none CC1CN(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)CC(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 121, 169, 169, 63, 63, 63, 21, 8, 1, 1, 1, 1, 1, 1, 1, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 169, 62, 21, 21, 8, 8, 169, 169, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 671 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581504 none CC1CN(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)CC(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 50, 169, 169, 169, 169, 169, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 7, 33, 33, 50, 50, 1, 1, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 39, 19, 20, 38, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 363 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581504 none CC1CN(C2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2)CC(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 1, 1, 23, 23, 23, 93, 108, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 6, 6, 23, 93, 93, 108, 108, 6, 6, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 40, 21, 22, 23, 24, 28, 29, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45]) total number of confs: 572 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581504 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581504 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581504/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581504 Building REAL300025581505 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581505' /scratch/stefan/7787361/working/building/REAL300025581505 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581505 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581505/0 /scratch/stefan/7787361/working/building/REAL300025581505 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1027 `/scratch/stefan/7787361/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC(Cl)=CC(Cl)=C1) `REAL300025581505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581505 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 11, 29, 29, 92, 96, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 29, 92, 92, 96, 96, 1, 1, 1] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25]) total number of confs: 526 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581505 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 19, 8, 1, 1, 1, 1, 1, 1, 1, 67, 146, 146, 201, 201, 201, 201, 201, 201, 201, 67, 19, 19, 8, 8, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581505 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581505 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581505/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581505 Building REAL300025581506 mkdir: created directory `/scratch/stefan/7787361/working/building/REAL300025581506' /scratch/stefan/7787361/working/building/REAL300025581506 /scratch/stefan/7787361/working /scratch/stefan/7787361 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025581506 mkdir: created directory `0' /scratch/stefan/7787361/working/building/REAL300025581506/0 /scratch/stefan/7787361/working/building/REAL300025581506 /scratch/stefan/7787361/working /scratch/stefan/7787361 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7787361/working/3D/1028 `/scratch/stefan/7787361/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CC=CC=C2)C1) `REAL300025581506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025581506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787361/working/building/REAL300025581506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581506 none CC1(C)CCC(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 58, 85, 174, 174, 174, 174, 174, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 58, 58, 85, 85, 3, 1, 1, 1, 1, 1, 3, 3] 174 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: 512 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581506 none CC1(C)CCC(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 174, 174, 84, 84, 84, 24, 8, 1, 1, 1, 1, 1, 1, 1, 174, 174, 174, 174, 174, 174, 174, 174, 174, 174, 174, 174, 174, 174, 174, 174, 174, 174, 174, 84, 25, 25, 8, 8, 174, 174, 174, 174, 174, 174, 174, 174] 174 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 545 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025581506 none CC1(C)CCC(C(=O)NCCC2=NC(=O)O[N-]2)C(C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 63, 174, 174, 174, 174, 174, 1, 1, 3, 3, 3, 3, 3, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 63, 63, 1, 3, 3, 3, 3, 3, 1, 1] 174 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 41, 34, 47, 48, 17, 18, 35, 24, 33, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787361/working/building/REAL300025581506 /scratch/stefan/7787361/working /scratch/stefan/7787361 Finished preparing REAL300025581506 Recording results /scratch/stefan/7787361/working /scratch/stefan/7787361 Appending to /scratch/stefan/7787361/finished/xaaaabe.* 0: /scratch/stefan/7787361/working/building/REAL300025581506/0.* Removing working files in /scratch/stefan/7787361/working/building/REAL300025581506 /scratch/stefan/7787361 Compressing combined databse files /scratch/stefan/7787361/finished/xaaaabe.db2.gz /scratch/stefan/7787361/finished/xaaaabe.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7787361/finished) ======================================================= Finalizing... removed `/scratch/stefan/7787361/working/3D/1029' removed directory: `/scratch/stefan/7787361/working/3D' `/scratch/stefan/7787361/working/protonate' -> `/scratch/stefan/7787361/archive' `/scratch/stefan/7787361/working/input-smiles.ism' -> `/scratch/stefan/7787361/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7787361/working/building' rmdir: removing directory, `/scratch/stefan/7787361/working' ls: No match. ls: No match.